I’d use the Wyrm Submersible Fortress (Mobile Structures rules) as a starting point. That way the base can operate on the surface or underwater as needed for research or to hide from prying eyes.
https://www.sarna.net/wiki/WyrmObviously a research version of the Wyrm would trade away some/most weapons, armor, and speed for more research capbilities and facilities. A really big base could be composed of several of these “submersible fortresses” operating together, much like buildings on a research campus or base of operations (think McMurdo in Antarctica).
A small fleet of VTOLs, WIGEs, hovercraft, hydrofoils, boats, subs, and/or even industrial mechs and sealed tracked tractors for the ocean floor could accompany and be housed by one or more “submersible fortresses”.
I’d even reference the Wyrm in the fluff. It didn’t come out of nowhere. Maybe on Terra the Blakies came across old plans for the Star League’s “Atlantis” Ocean Research Platforms (or ORPs — the last of which were operating rimward of Canopus...) and militarized the concept to create the Wyrm Submersible Fortress.
Some Wyrms like the Lowyfur were captured intact, so maybe the Republic demilitarized them as part of their swords-to-plowshares program, bringing back the Atlantis ORPs for research applications, at least on Terra.
Edit: Black Box technology might be another research focus for such a facility. The Star League supposedly gave it up in 2630 after HPGs came along, but that might just be a cover story. After the Blackout, the Republic no doubt would have pushed such research again.
https://www.sarna.net/wiki/Black_BoxAlso see Frobisher II if the rimward of Canopus reference wasn’t clear enough:
https://www.sarna.net/wiki/Frobisher