I noticed this with Water Protection on a Crystalite Elytra on the cape slot. The effects of the enchantment don't work when the elytra is in the cape slot, works fine in the armor slot.

#308 Mentions a similar issue with another enchantment.

I have also found that other effects such as getting lift from hydrothermal vents from the Better End mod don't work.

Mods need to implement enchantment checking themselves unfortunately, nothing trinkets can do.