That is certainly excellent! I have always kept the thought of conversion to UFO in mind. Only slightly related, I've just added the complex/facility map and it happens that TFTD ships fit under the pipes and walkways just fine:

I'm uploading the latest version I've got here with the lighthouse and main building maps, along with the basis for a UFO recovery version (no coast, no 'soldier' spawn points, more weight to natural terrain). The rest of the mod is still unstable since I was in the middle of adding new civilians which turned out to be way more of headache than expected. By the way, I'm seeing an issue along the coast in your screenshots which is to do with the first MCD entry in COLDISLEA1: it's supposed to be an invisible tile used to block access to the sea. I'm guessing the converter just deleted the entry from the pck file or something similar?
0.1.1
-Improvements to Polar Island terrain
-Canal added to beach urban
-Integrated map and route fixes from combo patch
-Modified Cargo ship part 1 with more spawn points so civilians don't look like they're being lined up to be shot
-Adapted Complex terrain as port terror
-Added more civilians
-Modified bikini civilian to work with randomized skintones and hair colours plus alt version in red bathing suit