When i place a enchanted book with say protection 1 it makes blank enchanted books with no enchantment , they just glow and are called enchanted book but u cant apply it to the armour ,

I see, then I will try implementing it by switching enable/disable in Config.

Since it could disrupt the balance, we are making sure to remove items with NBT.
I will support you if you have any requests.

I'm sorry but the "disrupt the balance" argument is kinda funny as disrupting the balance is exactly what project e and all its "family" do, not even the diminishing returns (or whatever it is called) config setting added when (or around) they finally stopped ignoring nbt, circa MC 1.15 iirc, helped!
IMHO adding nbt to project e was the best thing ever, it is wonderful being able to craft and enchant your perfect tool/weapon/armor, learn it and get a new one forever if anything happens. Its one of the very few mods that changed for the better instead of destroyed
So yeah this is my "vote" for adding nbt to item alchemy (along with all the other items ofc specially my beloved red katar :) )

P.S. A port of the ultimate un-balancer addon "Project EX" would also be superb ;)