In reply: Yes, you can use all the facilities at Atlantis while staying at the Comfort Inn. You can even read about it on Cruisecritic.com where people spending a day book a room at the CI to use the Atlantis property.
As to limitations due to tower, that did not exist when I was there. We used all the facilities which were just beautiful.
If you think something is not fair, think about how Atlantis charges a pretty penny for their "exlusive" resort and then allows cruise passengers to buy day passes. Not so exclusive after all.