Like title says, there's only a modifier for the loot and the scrap from containers and barrels but if you change the loot to "2" from "1", then things like guns or attire will also be multiplied by that factor. Is there any way to stop this from happening? There's a "Blacklist.json" in the Oxide data folder that just has the single entry "flares" in it. Would I have to manually add everything I don't want affected by the plugin?

you just want to multiple everything across the board and not change what's in containers then you don't need something like this. Check out https://umod.org/plugins/loot-multiplier. In that plugin you can block categories like weapons.

Honestly wish this was a feature in BetterLoot..