Thoughts on proposed house rule/setting clarification:
(1) Inquisitors are uncommon. Even in Scintilla, there aren't going to be hundreds of Inquisitors. The most common lead figure one would encounter would be an Interrogator or Interrogator Legate
(2) Inqusitorial power is, in reality, far far from absolute. The lack of a physically present Emperor making day to day decisions, combined vast size and slow/unreliable communications, means that actual power is a function of influence. A member of the Inquisition can certainly go to a planet and declare Exterminatus, but without the tacit/explicit support of other organizations it's unlikely to happen. Having a body of evidence, favors to exchange, reputation, or peers within the Ministorum, Astartes, Navy, or Administratum would be required before this could actually happen. Organizations within the Imperium are constantly "negotiating" power by exchanging assistance and temporary alliance
Mechanically, I'd represent this using Peers, along with Rank and something else (not sure what).