Ok good news enjoy the chaos! I'll be pretty busy today and tomorrow on contract work but I might have time tonight to finish testing the next version that includes the War Presets option and if I do I will release it.
Also for future reference, AW uses only entities and "things" provided by the game, apart from the various files it uses as part of configuration of what and how it does those things. Mods that alter the way the game works can certainly affect AW if those mods are doing strange things and are coded weird. But AW itself doesn't, because everything it touches in the game was created by the game itself. It simply reconfigures them as necessary for it to work. So my 1st hunch would be the explosions mod you refer to (I don't know anything about it) is probably detecting if the vehicle IsRequiredForMission and if it is it leaves it alone. Well, AW sets that flag to true on everything it scoops up which passes validation, because it has too. If it doesn't do that the game will randomly take the objects back and put them somewhere else in the world, so you would see things just disappear from in front of you, and also AW wouldn't be able to work at all because it would constantly lose objects it is working on and controlling. That wouldn't be much fun