When I was in Cozumel in Dec and Feb the tenders were shuttling back and forth all day. Some lines anchor off of Puerto Maya and their tenders bring people to shore there. Others anchor closer to town and tender passengers to the ferry pier downtown. Because they have to rely on tenders for now, Cozumel is only getting about half the number of ships they used to. I don't think you'll find the tendering to be too much of an incovenience. They seemed to have a good system in place.
If you book an excursion with the ship then you are usually on the first tenders or, ones that are reserved for specific excursion times.
If you book an excursion with the ship then you are usually on the first tenders or, ones that are reserved for specific excursion times.