Alf's Assistant says they're the same species, except Boombats have a more explosive diet. I can't think of any concrete evidence to suggest otherwise, except that Bats in AO seem to have long wings and a head separate from their body, whereas Boombats clearly are the reverse. The other side of the argument is that AO was the first glimpse into the Oddworld Universe and so Bats, while the same species as Boombats, weren't rendered accurately.
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