Just paste the following to your game's ini, but replace the last item,

"PrimalItemConsumable_RawMeat_Fish_C", with whatever your stacking mod's equivalent is.

ConfigOverrideItemCraftingCosts=(ItemClassString="PrimalItemConsumable_Bait_RawFishMeat_C",BaseCraftingResourceRequirements=((ResourceItemTypeString="PrimalItemResource_Fibers_C",BaseResourceRequirement=12.0,bCraftingRequireExactResourceType=false),(ResourceItemTypeString="PrimalItemResource_Sparkpowder_C",BaseResourceRequirement=2.0,bCraftingRequireExactResourceType=false),(ResourceItemTypeString="PrimalItemConsumable_RawMeat_Fish_C",BaseResourceRequirement=1.0,bCraftingRequireExactResourceType=false)))

From then just restart your server.

In the example below, I replaced
"PrimalItemConsumable_RawMeat_Fish_C" with "PrimalItemResource_Gem_Fertile_C", which now enables Fish Baits to be crafted using Green Gems.