The way the colonies seemed to function is defined by their distance from Mars in an era of no easy warp travel. The explorator fleets were sent out in intermittent periods of warp calm, and then cut off in the interim while they waited for gaps for them to return. Frankly the forgeworlds are really way too culturally-similar to Mars given the long separations, but this is just the nature of the scale of time in 40K.
It seems to me these worlds were functionally completely independent, and only lost that independence during the Great Crusade. But because of the nature of the Treaty of Mars that never meant much, because they were basically allowed to continue as before within the larger schema of the Adeptus Mechanicus and Imperium. Both should be treated as much as civilizations as actual states - they demand a baseline level of cultural, social, and political adherence, but beyond that do not have huge central management. And there was not much central management outright during the Age of Strife.
Lots of good thoughts. All I will note on the discussion of arks is the answer as to who it is already available to you.