Upon finding this out, is there a reason on why the extra NBT data that is applied to an item that has been added to the Tome, isn't stripped off when thrown out of the Tome?

This isn't really a bug but more of why that is not a thing.
It would be nice if the data was stripped off when the item is thrown out of the Tome so that any stackable items will stack again, but that is just a suggestion.

I will check if this is still relevant on 1.20