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In Sandy Mitchell's work, we see that (at least some) Space Marine chapters have a commissariat liason. They can't really give orders, but they can advise. I think that the relationship between the Salamanders and their liason would probably range the gamut from "Well, you just sit back at that space station, Mr. Commissar, and we'll call if we need you," (for more callous or bloodthirsty commissars) up to actually listening to their counsel, especially when dealing with the Imperial Guard. Nick Kyme's novels did a good job of showing us that just because the Salamanders put protecting humanity above their own personal glory, doesn't mean they are any better than the average astartes at relating to regular people. The wise commissars would work with the Salamanders as a conduit to bridge the gap between the two groups when the need arose.
When it comes to the Inquisition, I think that the Salamanders might butt heads with some of the more hardline Inquisitors over specifics, but they are still Space Marines, and still understand the need to make hard decisions. Even the most psychotic of Inquisitors probably won't try to call in a chapter of marines unless there's a good reason. I think that the Salamanders would be more inclined to evacuate (or quarantine) than to exterminate, but they would probably still understand that sometimes the needs of a couple of billion outweigh the needs of a few thousand.
Just my opinion, of course.
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