Click the item with flag "vanilla" will still run commands and other item flags seem to be still available.

Video
https://youtu.be/2q5QQ9PtiKg

Pastebin
https://pastebin.com/VRxF8SVd

Version
Paper version: git-Paper-439 (MC: 1.16.5) (Implementing API version 1.16.5-R0.1-SNAPSHOT)
ItemJoin version: v5.1.1-SNAPSHOT-b664

Additional context
Using ItemJoin is very useful to create custom item. The configuration is easy to setup. haha
According the wiki depiction, the flag "unbreakable" will may be invalid, but I want use it.
Can you also check it? XD

vanilla - Allows the giving of default unmodified no-name items. Please note if you choose to use commands or itemflags, etc. They will not function since all this does is allow ItemJoin to give a vanilla type item that can have a modified name or lore if defined.

Lol, I just love when a singular space that wasn't there before just magically appears.

Removing this space fixed the issue :) haha.

As for the itemflags, I will need to modify the wiki but only SOME itemflags will be made invalid, ones that are MODIFIERS will still apply. Such as attributes/unbreakable/always-give. Mainly the ones that stop working are self-drops, death-drops, inventory-modify etc. (Event itemflags). Hope that makes sense, ill probably need to write that in a more coherent way in the wiki.

Link to fixed snapshot; https://ci.craftationgaming.com/job/ItemJoin/667/
Remember to remove your old ItemJoin.jar file

This bug has been officially fixed in the release of ItemJoin v5.2.0.
You can grab it here; https://www.spigotmc.org/resources/itemjoin.12661/download?version=383801

Please read the changelog as the documentation has not been updated yet;
https://github.com/RockinChaos/ItemJoin/wiki/Recent-Changes