1. Start Arma with mods like Outlaw's Mag Repack, STHud, VTSGesture or VTSWeaponResting. (It's not dependant on the way to activate the mods, either via startup parameters, via the in-game menu or via an external launcher like Play WithSix. Equally it's the same in dev-branch and stable.)
2. Start a single player mission or the single player campaign.
3. Save game.
4. Resume to save game.
5. Notice that some mods (like the ones mentioned above) are no longer available in game although still being active in the main menu.