When I started writing this I realized that maybe I could add some other room and a hatch on that and it worked with a compartment. Up-to-date interactive Subnautica and Subnautica: Below. Then I went outside and it wouldn't let me add a hatch to any place on that room (it would let me on the finished ones though). Rooms and a Multipurpose Room, with an extensive network of catwalks found outside. Once I removed the ladder, finish what I wanted to do in the scanner room, I couldn't add a ladder back to the same spot, then I tried the other 3 places and it wouldn't let me either. I've just put a scanner room on the side of the ladder (didn't really think it would matter that much since I would remove the ladder once I finish). I've already built the bottom part but didn't have enough materials to finish the top part so I started the construction and left to do other things while collecting all the quartz I saw. I've prepared that to make a 2 floor height Alient Containment in grow creep and blood vines in my deep base. So I have 2 multipurpose rooms on top of each other.

It is possible however to add a compartment and a hatch on that. Go up it, build another aquarium and it'll auto-link to the one below it, rinse and repeat as many. Now build a ladder in one of the 4 slots that are against a wall, not in the center of the room. Stand just inside the hatch and build an aquarium (it's a tight fit). Got the room built, the connector built between them, and the ladder to go up. Mega, first stack your multipurpose rooms, then build a hatch into one of them.

Now it is impossible to build a ladder or a hatch in order to enter the multipurpose room and it is impossible to deconstruct either the room or the Alient Containment. So Ive been building my base in survival and wanted to have my personal room connected to the very middle of my base (at an X connector room) via a vertical connector. TL DR - I've partially built Alient Containment in a multipurpose room but removed the ladder into the room.

Subnautica multipurpose room bug