we looked around 4-5 temples but we couldn't find a Rogue Eye in it. My thoughts are that you replace LootTable of treasure chest with betterjungletemples:chests/treasure but other mods are using minecraft one to integrate with, so the eye is never spawned

or am i mistaken and there is a regular minecraft temple treasure chest somewhere in the other nbt's?

answering my own question: structure/challenge_room/challenge_room_statue_trade.nbt(or i assume any challenge room) has LootTable minecraft:chests/jungle_temple, so the integration should work fine, we are just unlucky :(