If changing factions and saving loadouts using Arsenal is allowed for a scenario, a loadout saved on one faction can be loaded after changing to another faction.
There probably is a faction change check in the game code that should factor for something like this and if there is, then it seems that such functionality isn't working completely.
I first noticed this behaviour while creating a scenario in Workbench. Just to be sure that this wasn't something that was only happening when testing via Workbench I did test the behaviour also on dedicated server and the issue was present there as well.