Let's just say they are really close, and yes, they are done in the same trip. Hol Chan is different in a few respects as it is a nature preserve (is that the right term), and you have to pay a few bucks to enter it. (you give your $$ to the captain, and he pays). Also, our guide snorkled with us at Hol Chan, and we had to stay with him at all times. At shark/ray alley we were free to snork around as we wished. At least this was my experience. Personally, I liked shark/ray alley more than Hol Chan, but I would go back to both. (I kept worrying that I was going to "lose" the guide at Hol Chan, and he was hard to keep in sight.)
Kathy