How to reproduce

1. Give yourself an item with a custom enchantment using:

   /give @s diamond{Enchantments:[{lvl:1s,id:"custom:enchantment"}]}
   

2. Place it in an anvil and rename it
   → See that the enchantment glow is now gone

Notes

Anvils can also not apply these custom enchantments either, if you combine an item which isn't enchanted with a custom enchanted item. (Enchanted book, same type of tool, etc.)
This is not WAI, as letting players work with custom enchantments without having to use vanilla enchantments is a powerful tool, which is really nice to have. Please keep it!