There are a couple holes in sector history that I would love to hear at least in-game theories on to ground some circumstances that are vague to the player.
These include:
The time between the Collapse and the arrival of the XIV to the Persean Sector. At this point, it's only the Luddic Church, Tri-Tachyon, indies, and pirates. Later, the Hegemony justifies its war over enforcing Domain-era restrictions on AI development by the threat of TT making a move fielding armadas of autonomous ships. But if TT wanted to conquer the sector, they had 48 years to do that before the XIV arrived where there was no opposition (outside of pirate warlords like Warlord Leonis, but I can't imagine them being a problem for TT if they wanted to clean them out themselves) and they themselves only started deploying AI warfleets in c84. What was the sector dynamic before the arrival of the XIV?
The lack of AI ships in the second AI war despite the existence of the remnants, which the public do not know about - but any spacer who has left the core and every major faction does. We have our own theories as to why TT couldn't levy these fleets after they lost the first AI war, but this isn't acknowledged by anyone as being convenient for the sector or inconvenient for TT. Though, the lack of them in the second AI war allows the official proclamation that they have all been destroyed to not fall apart. Very convenient, but again, why couldn't (or didn't) TT levy them? Isn't anybody (in-universe) bothered about this?
Domain leadership and discussion over the source of special Domain technology.
WHO is the source of Domain Restricted items? Who commands the battlegroups? The true-and-accurate-history mentions a Domain Sector-leader that prosecuted Ludd, but I doubt the leader of a frontier sector has power over the massive armada that occupied them to maintain control and stability (also, who in the Domain thought it was a good idea to time battlegroup rotations such that the first battlegroup leaves before anyone from the second battlegroup comes to replace them?). Who was above the Sector-leader, and likely the entity that had power over the gates? The Domain outsourced a lot of its technological development necessary for expansion to corporations, which includes terraforming technology, ships, communications equipment, as well as advanced AI. But we have Domain restricted items such as hypershunt taps and nanoforges which seem like their development, manufacturing, and distribution was entirely controlled by higher Domain authority and not a responsibility of a corporation (but the Domain didn't have such totalitarian control over AI, for whatever reason, especially given TT's multiple violations of alpha+ AI development in the past; I wonder how many people take notice to this part of their faction description). There are also the larger Domain megastructures - the gates and hypershunts themselves, which one wonders how they were made such that no one in the Persean Sector - or even the Domain military itself given how helpless the XIV were when they were cut off from using the gates - has any idea on how they work. Gates are massive and would require massive supply chains and logistics to supply resources and manufactured parts to build them, and we know there are a lot of them! How do you hide this process from human eyes unless you've automated the entire process without the need for human supervision...
(also, if gate haulers existed to haul gates, were there hypershunt haulers for the hypershunts?)