BetterLoot prefabs config
Can I remove the extra prefabs from the list of prefabs, so as not to change their loot, leaving only airdrop, codecrate and apk crate? Will the plugin work correctly? By the way, there are not enough barrels from RT in the list of prefabs. There are 4 types of barrels in the game.

No because the plugin keeps regenerating all WatchedPrefabs, seems like a bug to me, that should be possible. It will also keep generating 'default'(default is not correct either according to rustlabs) loottables for those containers in LootTables.json. The only thing you can do is set enabled to false for each container in your LootTables.json file.