It also affects the default loot tables eg: Strays drop uncraftable arrows and fishing yields uncraftable potions
The issue seems to be with loot tables not giving NBT data to the items. I have had similar issues with trying to convert my custom loot tables, and I confirmed it by fishing for a water bottle and getting an uncraftable potion (default loot tables)
It also affects the default loot tables eg: Strays drop uncraftable arrows and fishing yields uncraftable potions