The cyclops hatch is on the bottom and you can't block the prawn bay either, plus the cyclops isn't manevourable.
Moonpool would be too large and any enclosure would be a pain to park into and
He needs an underwater doghouse! Imagine on aurora you find the captain had a dog and you scan those items.
Build them external to the base and you could put a tank fish in it (crashfish is cuter imo)... and it will remain there.