On the editor I tried to change loot settings for military and civil spawn (while spawning in the airport [military] and some houses), it seems everything works, when I put 100% weapons in military, I only find weapons, and when I tried 100% survival items in houses (I mean 100% in civilian spawns), same thing, I find only surviving items, perhaps you just didn't put loot % settings correctly in the module. And don't forget to choose which buildings are included in your mission, in this case you should turn on A1 A2 A2:OA buildings at least and turn off A3 and A3:Apex [that's what I did].
About weapons, on my end it seems it's working correctly (I guess?) since I tried two times; one with RHS all items (weapons + equipment), other mods set only to spawn equipment and A3 limited, while choosing Chernarus preset, I only had new weapons from RHS (at least, not A3 weapons), second time I did the same thing with CUP while changing RHS to spawn only equipment (outfits) then another set of weapons was spawning ! (Since I don't know exactly what weapons are inherent to what mods, I can just say that between the two tests, the weapons set and ammo were different from each other and they weren't A3 default weapons).
For the wrecks and crates, I'm pretty sure it's related to civilian spawn % in the loot module settings (not 100% sure).
Hope it could help you @HMF
P.S: all what I said was tested on Chernarus WINTER.