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Just chiming in backing those supporting autonomy. Even the inquisition and lords of terra don't have official control of the adeptus astartes. Technically chapters are sovereign allied nations within the imperium able to accept or refuse requests at wish. The adeptus mechanus is in the same situation, an allied nation within the bounds of the imperium that can choose when and how to support them.

Many of the major powers of the imperium are set up this way: Rogue Traders, Inquisitors, navigators, ad-mech, adeptus astartes.

However, as with all politics in the imperil, the reality of this is dependent on any individuals or organizations actual power. A young or uninfluential chapter does not have enough power to stand up against an inquisitor who decides they don't like the cut of their jib. Likewise they need to keep the ad-mech happy as well as the navigator guilds.

Established chapters like the Ultramarines can largely do whatever they want. Unless they pull a Horus no other faction in the Imperium can afford to gainsay them.