Here's your issue:
- type: STR_ALIEN_BASE_ASSAULT
...
script: ALIEMBASEMAP
objectiveType: 3
nextStage: STR_ALIEN_BASE_ASSAULTUNDERGROUND
markerName: STR_ALIEN_BASE
markerIcon: 7
genMission:
STR_ALIEN_SUPPLY: 16
STR_ALIEN_BASE_UNDERWATER: 16 # <------------------------------------------------------------- here
STR_ALIEN_RESEARCH: 17
STR_ALIEN_HARVEST: 17
STR_ALIEN_ABDUCTION: 17
STR_ALIEN_INFILTRATION: 17
genMissionFreq: 6
The underwater base was created from a supply mission assigned to a land base (either Alien Base-1, -4, -8 or -9).
Region was taken from the location of the generating alien base... in your case completely randomly, since you have multiple regions overlapping on the entire globe... so OpenXcom has no clue, which region to use/take. If I see correctly both SEASPAWNS and LANDSPAWNS cover the entire globe (as first-class regions, not technical) and OpenXcom can randomly take them instead of vanilla regions.