Any recommendations on dive shops in these two cities that will sign off on PADI dives?
You might run into some difficulty in trying to get someone to agree to your plan. This is because most shops will want to sign you up for the full AOW course, so they can ensure the course is done correctly and they can then certify you as an AOW diver.
There is more to the AOW course than simply "do a dive, sign me off, repeat." There are performance requirements for each dive that are preceeded by classroom (or online) work with your instructor.
Any PADI shop
can arrange for you to work with an instructor. How willing they are to do so just for one or two of the five AOW dives, and how much they will want to charge you for it, just depends on the shop.
As for shops... as the previous reply mentions above, there are a lot of shops on Roatan. I think the closest one to the cruise ship docks is probably Barefoot Divers. Most shops are on the west end of the island, which is a little further from the cruise ship docks. Just search online for Roatan dive shops and you'll see what pops up.
In Belize City... just the opposite. I've been there on a cruise ship stop and from what I understand there is only one dive shop in the city, Sea Sports Belize. We dove with them. Nice people, but definitely not concerned with keeping a schedule. Very laid back. Maybe not the kind of shop that handles special requests well.
Is there a particular reason that you want to do your AOW this way? If it's just to get the AOW card as quickly as possible, then I would agree you're going about it the right way. If you're actually interested in quality training... you might want to reconsider taking the entire course with one instructor that can integrate all five dives into a cohesive course and really give you something worth paying for.