I don't think so. The way the workshop works, if you can get foils, you can put colony pods on them. I presume you want to allow both foils and colony pods.
What you can do is, make sea tiles useless. I.e.,
no nutrients, no energy, no minerals. Then make improvements (mine/kelp/tidal thingy) take 200 turns each, and/or require Threshhold of Transcendance to build.
I see two problems with my suggested approach. (1) The AI may try to build sea bases anyway. (2) You'd need to know how to do all this, and I haven't a clue.
Of course, you could presumably make all sea tiles 'ocean depths' and not shelf tiles. Then only the Pirates can build there, and obviously they would not be in such a scenario. The problem with this idea is, if the water level changes, you could end up with shelf tiles again.
Hope this helps.