The portals are all gates into Oblivion. The Shivering Isles, Boethiah's and Peryite's realms are all planes of Oblivion, just like Mehrunes Dagon's. Martin was closing the link between the places.
The portals to the Shivering Isles, Beothiah's realm, and Peryite's realm were fundamentally different from the portals to Dagon's Deadlands. They were friendly portals. The portals to the Deadlands allowed Daedra to escape and were opened with the intent of invading Mundus. The portals to the other three realms were opened willing under friendly terms for mortals to enter and exit freely. There is no rule or law that prevents that from happened, provided that these portals remain friendly.
Haskill, when asked about the Door:
"It poses no danger to Mundus; no compact has been violated. It is a doorway, an invitation."