I don't exactly know if this will help but this is the best I can offer for editing the loot of beasons in this mod. I will share the file path and file name of several LootItemSets that the game calls on and you should be able to replace those with your own through the ini.

Here is the file path for all LootItemSet files:
Game/Mods/EndGameBeacons/ItemLootSets/

Here are a few of the files (the mod uses 67 so I'm not listing them all):
LootItemSet_EGB_CaveNotes
LootItemSet_EGB_CaveNotesAB
LootItemSet_EGB_CaveNotesEX
LootItemSet_EGB_CaveNotesSE
(the above just drop cave notes and will probably be your best choice to replace. AB/EX/SE are map specific)

LootItemSet_EGB_AmmoHigh
LootItemSet_EGB_AmmoLow
LootItemSet_EGB_AmmoMed
LootItemSet_EGB_AmmoRare

LootItemSet_EGB_WeapHigh
LootItemSet_EGB_WeapLow
LootItemSet_EGB_WeapMed

LootItemSet_EGB_StructureWood
LootItemSet_EGB_StructureMetal
LootItemSet_EGB_StructureStone


Combine the file path with the file to get what you want to swap:
"Game/Mods/EndGameBeacons/ItemLootSets/LootItemSet_EGB_CaveNotes"

Again, I don't know exactly how that's done, so you will have to look elsewhere for help.