"I notice there aren't many rules for Mercenary 100%, and so I wanted to check first. Is it merely a complete playthrough, without abusing glitches?"

Yeah, that is that category.

"If so, similar to my post in the MW2 forum, would a submission be okay as long as it is a recording of the game from start to finish, even if reloads are necessary for mission failures?"

Yes! That's perfectly fine. Obviously verification would be looking into whether or not you load into a different save, but it shouldn't be an issue. Good luck with your run~

Those timings are pretty standard throughout the series as it's the moment you gain control within the game and the moment you lose control at the end.

Would Mercenary be a true 100% or just a glitchless any%?