If you did it with custom markup, sure it would break something. But it should be doable just with styling IIRC, in which case it shouldn't be able to break anything.
(Mind you, I have in one project actually implemented totally manual checkboxes before now, wasn't that much work and worked really well, IMO, better than using actual checkbox elements at least, heh. But I specifically didn't have to care about accessibility or anything like that)