I've updated the mod, but beacon interfaces still don't work. I even tried editing the Beacon Interface mod so it defined its module category in data.lua instead of data-final-fixes, but there's no change. It looks like the beacons are correctly given their module category, but every other machine in the game is still blocked from that module category. Which is odd, because it looks like the category should be in the base_module_categories list which you give to all entities.
Maybe you can get around the issue by adding a fake 'effect' to the Voidcraft modules instead. Then instead of adding module categories for every entity, you can just set the allowed_effects of your own machines to allow the new effect, and on all other machines the effect would default to being blocked. I'm not sure if it's even possible to add a new effect like that, though.