Different operators leave at different locations. If we visit Palancar caves, for example, it is shorter from the Fonatur Marina than the Aqua Safari Pier. Barracuda, San Juan and Cantarel from Fonatur are going to be a drive south to Fonatur and then a boat ride back north, and a shorter distance from Aqua Safari.
Should this be a consideration selecting an operator? If I want to see the Northern sites, am I better picking someone who leaves from Aqua Safari? Does anyone do the Northern dive sites in Winter? If I know I mainly going South, do I save time choosing someone with a southern departure?
I would say that this should not be a consideration.
From my perspective, there are 2 basic things to balance -- where you want to stay (center of town is my preference, for walking access to a great variety of restaurants) and the type of operator you want to dive with.
Few operators regularly go to the northern sites, despite several listing that as an option on their websites. You will almost always be going south, except for special trips.
For me, once I'm on the boat, I generally don't mind the extra few minutes in either direction*.
Staying north of the airport is going to be the most problematic location -- except for a few dive ops, you'll have to make your way down to the Aqua Safari pier or the marina. Similar consideration for staying "in town", though it's easier/cheaper to get a taxi to the marina and some operators will [informally, contravening the taxi regulations] arrange ground transportation.
Staying south of the marina....most operators can arrange a pickup at a hotel pier as they head to southern dive sites in the marine park. Of course, on the infrequent occasions that you're diving north of your hotel (northern site out of the park, night dive), you'll probably need to get yourself to the marina or the Aqua Safari pier.
* I hope that Aldora has changed their routine, so that customers don't get on the boat at the Aqua Safari pier, go north to the Aldora Villa, then head south past the Aqua Safari pier without stopping, and the reverse on the way back -- dropping customers at the Villa off before ending the day at the Aqua Safari pier.