The slots we're displaying are not real slots, so mods such as JEI and REI are unable to detect that they are displaying an item. Ideally, we can somehow let these mods know that we're displaying a slot that can be queried by them for showing recipe usages.

Looks like both JEI and REI have support for registering hooks for this purpose:
REI: https://github.com/shedaniel/RoughlyEnoughItems/blob/6524d9a4aa1fb83e097f4754f1d82b7044cef5cb/api/src/main/java/me/shedaniel/rei/api/client/registry/screen/ScreenRegistry.java#L79-L84

JEI: https://github.com/mezz/JustEnoughItems/blob/566c4a7ffba1556b39ba37a146ff6696a422e9c1/src/api/java/mezz/jei/api/gui/handlers/IGuiContainerHandler.java#L29-L43