Speaking of markets, is there any chance you could make the Idoneus Citadel Garrison non-hostile to the Luddic Church? An odd request, I know, but hear me out.
Eos is the primary food producer of known space, but even trading small amounts of food there can be a devastating reputation loss due to Idoneus' hostility to the Luddic Church. For us focusing on trade, we either have to make the Idoneus hostile or lose access to the entire Eos market -- a grave loss given the importance of food shortage trade runs. I don't think any other system produces enough food to meet the demands of those 10000 foodstuff shortfalls on major worlds.
Most other mods have their bases and planets contained to distinct systems to prevent the disruption of vanilla Starsector trade and activity, so this has never been an issue for me before, even with other mods featuring factions hostile to one another. At least with the Colony fleet you can wait until they leave a system to resume trading there, but with the garrison, the denial of trade (without loss of faction reputation) is largely permanent as they do not move.