Sorry but i dont understand what you mean. What mods? The Tribut Transfer Mod includes the vanilla trophys too, so you can apply them in the converter.
All packages are tested with the required items, trophys and artifacts and seems to work fine. please give me a concrete example

You have 4 trophy for just megapitecus
uou have Gamma Beta and Alpha and you have vanilla are not difficulty
i send you spawn code for and for all other

Vanilla (he not have difficult befor) "Blueprint'/Game/PrimalEarth/CoreBlueprints/Items/Trophies/PrimalItemTrophy_Gorilla.PrimalItemTrophy_Gorilla'"

Gamma
"Blueprint'/Game/PrimalEarth/CoreBlueprints/Items/Trophies/PrimalItemTrophy_Gorilla_Gamma.PrimalItemTrophy_Gorilla_Gamma'"

Beta "Blueprint'/Game/PrimalEarth/CoreBlueprints/Items/Trophies/PrimalItemTrophy_Gorilla_Beta.PrimalItemTrophy_Gorilla_Beta'"

Alpha
"Blueprint'/Game/PrimalEarth/CoreBlueprints/Items/Trophies/PrimalItemTrophy_Gorilla_Alpha.PrimalItemTrophy_Gorilla_Alpha'"

Sorry for my bad english

I have checked this again and can confirm that with Megapithecus, Broodmother, Dragon and Manticore all 4 Trophys can be put into the converter!

For me, All Trophy Gamma Beta and Alpha work for All Boss but trophies that are not named Gamma beta or alpha do not work

Megapitecus
"Blueprint'/Game/PrimalEarth/CoreBlueprints/Items/Trophies/PrimalItemTrophy_Gorilla.PrimalItemTrophy_Gorilla'"

BroodMother
"Blueprint'/Game/PrimalEarth/CoreBlueprints/Items/Trophies/PrimalItemTrophy_Broodmother.PrimalItemTrophy_Broodmother'"

Dragon "Blueprint'/Game/PrimalEarth/CoreBlueprints/Items/Trophies/PrimalItemTrophy_Dragon.PrimalItemTrophy_Dragon'"

Manticor
"Blueprint'/Game/ScorchedEarth/Structures/TrophyHeads/Manticore_Trophy/PrimalItemTrophy_Manticore.PrimalItemTrophy_Manticore'"

All this Trophy arenot converter in your mod

Now I see what you mean. I thought you couldn't put the trophy in the converter. The Vanilla Trophys cannot and do not have to be converted, because they are transferable.

Where you come from?

i from french
and its not transferable its probably modded trophy from mod annunaki reborn