My temptation, based on fluff, would be to say that if you can set your chapter's initial relation with factions, it should probably be a mostly fixed point with mostly elastic variations if you're an established chapter - you're riding thousands of years of reputation, and the other parties are thousands-of-year-old bureaucracies. Permanent relation changes - for better and worse - should be small and hard to effect, and temporary ones should have diminishing returns the further you get from your permanent equilibrium point. New chapters, OTOH, should be more flexible and have an easier time changing their reputations and relations due to a lack of inertia.
For what it's worth, my vision for faction interactions (which I'm nowhere near implementing yet) will have tiers... personal relationships, "local" relationships, and faction relationships. The higher the level, the smaller the movement. So, for example, if an Inquisitor asks the chapter for assistance, and the CM sends a squad of marines, and things go well, a bunch of things happen:
1) The inquisitor's opinion of those particular marines goes up a lot
2) The inquisitor's opinion of the chapter goes up some
3) The inquisitor's opinion of astartes generally goes up a little
4) The Ordo the inquisitor belongs to has their opinion of the chapter go up a little
5) The Inquisition as a whole has their opinion of the chapter go up a very small amount
So, if the same inquisitor comes back again, maybe he requests one of the specific marines he worked with previously, or expresses his sadness at hearing that one of the ones he worked with previously died in battle. If a different Inquisitor needs assistance, maybe he mentions the positive interaction the previous inquisitor had. And so on.
But, that's all down the road. For now, the immediate reputation system will probably only involve planetary governors, and have other forces and factions added in as I add them. I don't have a design in mind yet for how to make this part of the logic more moddable, so it'll take some pondering as I head in that direction.
Also keep in mind that the default gameplay I'm building today is a newly-founded chapter, so not much pre-build reputation with anyone beyond the normal respect shown to the Emperor's Chosen. Also, the hope is for thousands of turns of play (hundreds of years) with a single chapter. Over time, larger reputation movement should be possible.