If a mod has an item similar to a shulker box that also has the lore of the items, there is no way to remove them and have continued compatibility with your mod.

I believe that line 58 in ItemStackMixin is where the issue is, as you are brute-forcing a check for it to be a vanilla shulkerbox.

Im not here to tell you how to fix this issue, but a tag or some form of registering system like with the view providers might work.

These checks were introduced in order to fix issues with shulker preview datapacks, I'll remove them as part of the 3.0 API changes.

Lore removal is now controlled by a configuration option (which is off by default).
I'm closing this issue.