I'm not a mod, but since you did all the maps in a category together, I don't see why this would be an issue. Nothing carries over between maps in Instant Action, so it doesn't give you any advantage. You'd basically just be treating the other categories as IL's. It's also be worth noting that this would be an extra incentive to do 100% runs.

Just out of curiosity, how long do you think the full 100% run would've taken you?

As long as there isnt any maps that are not part of that category in between what you want to submit (ex: do not have bunch of hunt missons in between the conquest missions if you want to submit a conquest run). I dont see any issues with that. :)

I kinda did the same thing for a Kashyyyk IL submission which I took the footage from one of my old full game PBs because I really did not felt like doing actually ILs attempts lol (because Kashyyyk is a 10 minutes auto-scroller for those who do not know).

And yeah there is absolutely no reasons to turn friendly fire off in general for speed runs. Your allies' grenades wont be able to damage you anyway, you just have to worry about not killing your own self lol.

I have been doing a bunch of CTF runs this week and sometimes I end missions with like minus 40 points because my teamates keep picking up the flags.

Estimate for a godlike 100% here would be sub 3:30:00, but would be extremely lucky haha

Average time for a runner of all categories in 100% would be in the 4 hour mark