Ah ok thanks for the links that especially helps!
To answer regarding ECM: hopefully? The past link was about the skill not unapplying I thought- because it was removed via console commands (which presumably doesn't call the relevant code). The fact that the bonus was 0% was not intended as it was supposed to be 5% (or half of the standard value).
That part has been fixed at least. If you are respeccing skills via the normal method and the 5% bonus (instead of 10%) is still showing up under the same circumstances, then that is a separate issue that I'll need to try and handle if I can.
The faction d-mod issue: Ok I remember that post now sorry there has been a lot of feedback in the last few months and I'm sure that isn't the only thing slipping through the cracks.

So just to continue to narrow things down, was this a vanilla issue that was/is being fixed and now I should account for that in faction balance, or is this issue still at large in the current version? To be honest, if its the latter then I'm not really sure what could be causing it other than possibly a miscommunication of the UI regarding the actual d-mod chance. It certainly doesn't seem to meet the average based upon the screenshots though.
From the technical side of things, the only thing I do regarding faction quality is set the quality of the faction for the new factions and in some systems I obviously include nanoforges - including a couple additions to vanilla factions iirc. Though nanoforges are accounted when displaying overall ship quality afaik, so that wouldn't explain the discrepancy.
I'll try and investigate a bit tomorrow when I also look into bomber stuff that was relatively recently discussed. That's the current plan anyway. I spent quite a bit of time diving into more skill work today and I'm feeling pretty satisfied with the final-ish results. Once I'm 100% sure I'm done I will post some screenshots of the changes - there are specifically a lot of changes to Industry to discuss/showcase.
I've also completed ~75% of the new variants for the new ships that came with the last official Starsector update.