It is possible this is more related to config structures then Alive, but it is a result of the Orbat tool.
I have been creating one blufor and one opfor faction in the Orbat tool and made them into two separate PBO-files. They work fine on their own, but having both in the modset causes the alphabetically lower one to not exist in-game. I have tried to make a single Hpp-file with both faction configs in it, but this as well only causes the one put in first to exist or cause fatal errors when starting the game.
It should be noted this is my first serious dive into Arma 3 configs, so it could be that I am missing something obvious, but after messing around with this for the better part of the day and looking around for solutions, I will just see if anyone here has suggestions.
Edit: After further reading of the general Orbat-thread, I located the same issue and found the response to it, it was related to the mods still technically being named @testmod, so after renaming and repacking it is now working as intended.