I don't see why the Vykkers can't go underwater. Vykkers Labs 12 was the first fully free-floating structure, before that they're facilities must have been on the ground (or tethered). I wouldn't say they love heights - more have a subconscious drive towards them. But then maybe that isn't a submarine. It looks like it could be one to me. The chimneys could be to release anything: a kind of aquatic Poop Chute.
At least, it doesn't look airborne to me. I'd always seen it as making sense, since ME is meant to be about what Munch does with the eggs - which require water, after all.
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