It's a shame blocks like Quark's cave crystals and Aether Legacy's Aerclouds aren't chiselable. Even if you force it through adding it in the JSON they become solid. Would it be possible to support chisel textures for said blocks at some point, with translucency kept?

Not easily enough.

Would it be possible to do so manually? I wouldn't mind needing to fiddle with a json myself to make certian textures semi-transparent. I understand automatically doing so would be a nightmare and a half, but chisel does support colored glass by default, so it has to be in some way possible?
Or am I misunderstanding the situation entirely?

@notdonte you have piqued my interest.