The restriction on owning property in Mexico adjacent to the shoreline does not apply to companies, only individuals. As a foreigner in Mexico, you could form a Mexican company and then have your company buy the land, as did Vulcan years ago. Vulcan was extracting limestone and shipping it to the US for processing.
That is correct. Most of the quarry (not all of it) and the port are on Cozumel's mainland enclave of Rancho Ina. Cozumel still has two mainland enclaves. One is made up of two parcels, the Rancho Ina (aka Punta Venado) and the La Rosita quarry (for a total of 2,802.716 acres), The other enclave is Xelha (209.26 acres). You can read all about these enclaves, their histories, and the Maya ruins that are on them in my newest book, The True History of Playa del Carmen, available as an eBook or paperback on Amazon books.