Question of Loyalty adds ranks and bonuses to commissions, but you also can only ever own a few colonies at a time, can't experience colony crisis events since those colonies/markets are owned by the commissioned faction, which for people tired of the PL crisis, is probably a bonus in their eyes. Free storage at all markets owned by your parent faction, you can eventually tell patrols to not bother scanning you, you can scan cargo of smugglers in/near markets owned by your parent faction. Either way, here's the ranks and the descriptions in a top-to-bottom list, from lowest rank to highest rank:
Rank 1. Accountant - "Newly invited into Tri-Tachyon Special Circumstances, hopes from those above you are quite high for your potential. Of course the expectations that you'll succeed are even higher, and higher still is the penalty for failure to carry out your tasks in an acceptable manner."
Rank 2. Senior Accountant - "You've shown you can handle the more simple tasks given to you by Special Circumstances, your promotion has given you a bit more leeway in carrying out the orders from up top; but only a bit, you're still being heavily monitored to ensure your invitation was not a mistake that has to be corrected."
Rank 3. Problem Solver - "More jobs, more smuggling, more wetwork to be done. Those high up at Special Circumstances are starting to view you as someone who is quite adept at solving small problems whenever they crop up, you'll need to prove that you're capable of more than just the small ones though if you don't want to end up 'retired'."
Rank 4. Procurement Specialist - "Whether it be a report on a successful delivery of cargo, extracting wayward employees or competitors, or even just tactically bombarding markets to increase profit margins, you've shown you can be trusted to perform and not get caught. Even if you do get caught during whatever job you've been tasked with, your superiors know you've no qualms about dealing with any whistleblowers from within or outside of Tri-Tachyon and Special Circumstances."
Rank 5. Human Resources Manager - "The hard part isn't getting rid of problems these days, it's having to file all the reports from people failing underneath you, whether they be employees of Tri-Tachyon, incompetent members of Special Circumstances that need to be culled for the sake of reputation, or even just a quartermaster who asks one too many questions. You're at the point where you look forward to simple smuggling or assassinations, there's far less menial reports involved."
Rank 6. Executive Auditor - "The board trusts you when it comes to the most unpleasant acts that need to be carried out, a great deal of leeway is even given to you by Special Circumstances so long as you continue to advance their goals with both results and profits. You've gotten pretty good at 'cooking the books' too in such a way that it doesn't lead back to you... the dead can't file any complaints after all."
Rank 7. Enforcer of The Board - "Finally, you've reached the point of being absolutely indispensable to both Tri-Tachyon Special Circumstances and The Board itself, not just through your ruthless efficiency, but hushed whispers of how even the few superiors above you are afraid of getting on your bad side. High Executives of the more public-facing part of the company sieze up in quiet terror whenever you enter the room or see you on their comms, to say nothing of those beneath your rank. The entire Board knows and fully approves of your use of installing and making use of Alpha-level cores into your ships, it makes dealing with those who get in the way that much easier and efficient."
That bit about Alpha cores being integrated is from one of Yunru's mods more than anything else, really. I actually had a lot of fun thinking them up and writing them out, I hope you like them as much as I do. Like I said, it goes from very Corporate-speak to becoming more Mask-Off in what TTSC is about, with the final rank just dispensing with pleasantries entirely.
Whoah, this is awesome thank you for taking the time to type it all up and share with me. I just got back from running some errands and was about to play test a Hiver/Stelnt combo volt and I are working on but saw I had a reply here. I figured OK I'll just pop over to TTSC first and see what's up. I have spent quite some time now reading and re-reading this and it has prompted me to investigate question of loyalty now to see if I can incorporate my mods into it (well at least this mod since some hero has done 90% of the work already) 
To get those ranks and such to display properly you have to go into Starsector\mods\Ashes of the Domain - Question of Loyalty\data\campaign\aotd_commision_data.csv and add this line at the bottom, preferably in Notepad++, here:
TTSC,"accountant, senior_accountant, problem_solver, procurement_specialist, human_resources_manager, executive_auditor, enforcer_of_the_board","accountant:0, senior_accountant:250, problem_solver:500, procurement_specialist:750, human_resources_manager:850, executive_auditor:1200, enforcer_of_the_board:1700",,2000,,
It has to be exactly like that, and TTSC is in all caps because that's how it's used in your factions.csv file. Once you do that, you have to edit aotd_rank_data.csv file in the same folder to look like this and the start of each new rank requires it's own line, so you probably shouldn't do a straight copy/paste, do it for each individual rank entry:
accountant,Accountant,5000,true,2,0,10,2,"can_scan_cargo,free_storage","Newly invited into Tri-Tachyon Special Circumstances, hopes from those above you are quite high for your potential. Of course the expectations that you'll succeed are even higher, and higher still is the penalty for failure to carry out your tasks in an acceptable manner."
senior_accountant,Senior Accountant,10000,true,5,0,30,3,"can_restock,can_scan_cargo,free_storage","You've shown you can handle the more simple tasks given to you by Special Circumstances, your promotion has given you a bit more leeway in carrying out the orders from up top; but only a bit, you're still being heavily monitored to ensure your invitation was not a mistake that has to be corrected."
problem_solver,Problem Solver,20000,true,7,1,40,4,"can_restock,can_intimidate,can_scan_cargo,free_storage,have_research_permit,can_retire","More jobs, more smuggling, more wetwork to be done. Those high up at Special Circumstances are starting to view you as someone who is quite adept at solving small problems whenever they crop up, you'll need to prove that you're capable of more than just the small ones though if you don't want to end up 'retired'."
procurement_specialist,Procurement Specialist,50000,true,9,1,80,5,"can_restock,can_intimidate,can_scan_cargo,free_storage,have_research_permit,faction_blueprint_access","Whether it be a report on a successful delivery of cargo, extracting wayward employees or competitors, or even just tactically bombarding markets to increase profit margins, you've shown you can be trusted to perform and not get caught. Even if you do get caught during whatever job you've been tasked with, your superiors know you've no qualms about dealing with any whistleblowers from within or outside of Tri-Tachyon and Special Circumstances."
human_resources_manager,Human Resources Manager,120000,false,11,2,150,5,"can_retire,can_intimidate,gets_colony_protection,have_research_permit,can_scan_cargo,free_storage,faction_blueprint_access","The hard part isn't getting rid of problems these days, it's having to file all the reports from people failing underneath you, whether they be employees of Tri-Tachyon, incompetent members of Special Circumstances that need to be culled for the sake of reputation, or even just a quartermaster who asks one too many questions. You're at the point where you look forward to simple smuggling or assassinations, there's far less menial reports involved."
executive_auditor,Executive Auditor,150000,false,13,2,200,6,"can_retire,can_intimidate,gets_colony_protection,have_research_permit,can_restock,can_scan_cargo,free_storage,faction_blueprint_access","The board trusts you when it comes to the most unpleasant acts that need to be carried out, a great deal of leeway is even given to you by Special Circumstances so long as you continue to advance their goals with both results and profits. You've gotten pretty good at 'cooking the books' too in such a way that it doesn't lead back to you... the dead can't file any complaints after all."
enforcer_of_the_board,Enforcer of The Board,200000,false,15,3,200,1,"can_retire,can_intimidate,gets_colony_protection,have_research_permit,can_restock,can_scan_cargo,free_storage,faction_blueprint_access","Finally, you've reached the point of being absolutely indispensable to both Tri-Tachyon Special Circumstances and The Board itself, not just through your ruthless efficiency, but hushed whispers of how even the few superiors above you are afraid of getting on your bad side. High Executives of the more public-facing part of the company sieze up in quiet terror whenever you enter the room or see you on their comms, to say nothing of those beneath your rank. The entire Board knows and fully approves of your use of installing and making use of Alpha-level cores into your ships, it makes dealing with those who get in the way that much easier and efficient."
You also need to make sure the correct number of commas separate each faction's entries as their own line entries, you'll see what I mean as soon as you look at the specific file.
,,,,,,,,,
That is the correct number of commas to be placed above and below the rank entries in the aotd_rank_data.csv file. You'll be able to see the changes mid-save and you can tweak most things mid-save until you find a balance you like. I personally run SOTF so I make it so I can run one extra market/colony compared to base QoL numbers so I can run that colony in the Duskkeeper star system with no real penalty.