Whenever custom items are enchanted, they will have some kind of glow effect. But for custom items that only have their default enchantments, this is not always desirable. Unfortunately, I don't think this will be very easy to implement.

I don't think it'll be too difficult, unless I'm missing something you could use ProtocolLib to clear the enchantment NBT, and add replacement lore. ProtocolLib has an ItemDisguise example showing how to filter enchantments from item meta.
Only problem with this solution is I'm not sure if you can do unlocalized strings for item lore. Something to investigate at least.

It looks like that solution is based on packets, which is potentially a threat (typically minecraft-version-dependent, so we need to be careful with such things).
When the time comes, this is definitely something to investigate, but there are 47 other issues...