Is it even worth it to think about making hijack only do this if the player's running, or if it's not coming from the shell, or any other hacky things like that?

With all due respect, I'd personally put this in the "Doc, it hurts when I do this" category. The solution is "don't do that." Now that you know the nature of the problem, you won't do it again. It seems to me any attempts to enable/disable the fid-mangling logic based on who's looking or who's copying or what's running at the time would be hackish at best, and dangerous to normal player/synchronization operations at worst. Your situation of wanting to manually move FIDs around to make space to do file taxiing seems isolated, so I don't know if it's worth creating a special case for in a kernel that we all use.

I don't say this to torpedo your request, but, frankly, I know of a lot of other things on the Hijack wish list that I'd rather see, and have a much larger potential benefit.