I have a custom model working for an object
(tested with /give @s minecraft:item{CustomModelData:1} )

I have modified the loot table of the oak leaves in a jungle leaves one (replacing leaves and sappling) and changed the apple to the custom model with "set_nbt".

All should work according to various people I asked, but it doesn't.

When I just modify oak in jungle, I get all drops written including apples. The moment I add nbt, only sapplings and sticks remains, no apples (vanilla or custom model)

Searching here lead to a similar issue back in 1.12, but marked as resolved. I think now that blocks also have loot tables, it could be tied.

Similar issue resolved 1.12 MC-122536

loot_table attached