I have the exact same phobia as you, OP, and I have no idea where it comes from, really. I also have a phobia around large industrial machinery, so my ultimate nightmare is being trapped on an oil rig or something similar in the middle of the ocean. I haven’t tried Subnautica yet, but I’m interested to see if it will trigger those same fears for me that it did for you.
I think I have the same sort of reaction you’re discussing around a lot of horror games. I often find myself wanting to play them because I’m a bit of a low-grade horror film fan (there’s a very specific kind of horror I enjoy), but something about actually having to play out a horror story myself sets my nerves on edge in a serious way. (The most recent example of this is Kitty Horrorshow’s “Anatomy,” which I only just managed to finish because of its length…although I was sort of a nervous wreck by the time I got there.)
I go back and forth with this. I’ll completely avoid horror games for a while, but then something will come along that piques my interest and I’ll go ahead and give it a shot. Sometimes I mange to push through because I’m so fascinated by what’s going on in the narrative (as in the Silent Hill games) and sometimes I just can’t do it (as in Amnesia).
I’d like to think eventually I’ll overcome these fears, but history has sort of proven that untrue. I don’t know if continuing to play them really helps or not, but I have no doubt I’ll continue to do it.