I picked up the addon earlier today by request by some members of my server.  And instantly recieved complaints about the "elite crates" (an example, the ones at the top of the dome) dropping crap, like fish, and pumpkins and just generally garbage.  Those are not regular crates so they shoudlnt be governed as such.  But they appear to be.  Id like those crates to drop one tier under Bradly crates or the UNlockable Heli drop crates.  But... they are basically bottom tier crates by default.

You can change the amounts and types of loot in crates but the plugin will not change the class/tier of crates from their default value, They are not a "specific" crate like the bradley, heli or supply drop so if you change the contents of the crates it will of course change the contents of all that tier of crates.
You can do what i do and go through the entire data lootlist and change all the loot to what is required by you and your players and remove those items that you dont want to appear by using the blacklist (in the CONFIG json file)