Figured I should just dig up the XBLA-related thread I already made instead of starting a new one for a minor update.
So, I asked Bruce Morrison on Twitter about those sketches; in the early stages of porting, there were ideas for enemy variants (obvious with the F'lickta, but I didn't know about others) and a female Security Officer. Most of these were scrapped, but they did keep the M1!S'pht.
Relevant tweets: 1, 2, 3, 4.
The doodle of Leela was probably just that, though, so it doesn't seem like they planned to show the AIs.
Also, unrelated thoughts posted to the ManUpTime Studios site.