This thread, from the archives, is not exactly a bug list, but it's close. Unfortunately, the actual bug list (whose link appears in the first post of the above thread) no longer exists. Some of the bugs reported in the thread were fixed in subsequent patches.
I loaded your save file and verified your understanding. I also remember building sea bases in ocean trenches in other games.Specifically, for SMAC (Mac version fully patched; SMAX installed), the manual (Chapter 3, Terrain, Oceans, p. 41 in my version - this may be a Windows version I picked up for a dollar) says: "Ocean and ocean trench squares can not support bases or be enhanced."
I've confirmed that ocean and ocean trench squares can not be enhanced. However, I have been able to establish bases in both ocean and ocean trench squares.
I would appreciate:
(1) links to comprehensive bug lists besides the SMAC Academy and the AC Creation lists.
(2) a verification about establishing bases in ocean and ocean trench squares. You can test with the ACDG5 2188 turn. Windows users won't be able to save it because it was generated on a Mac, but they'll be able to move sea formers around and establish sea bases with the sea colony pods.
I was going to install an unpatched version of SMAC to see if the information in the manual was changed in a patch. Can't find my disc right now. I'll try this if the disc shows up.
Petek(3) links to any post reporting that the poster was able to establish a sea base in SMAC on an ocean or ocean trench square.