The genesis of this mod was taking Spidertron Engineer and refactoring the code a whole bunch because it was pretty close to what I wanted to start with, but I wanted to strip out all the "you ARE a spidertron" bits. That being said, I'm not sure how important the new surface parts are to this mod anymore. I think the intent there was to ensure that if/when you went to a new surface (there was some in-built support for SE) that a spidertron would be properly spawned if you were inside it.
I think it's probably safe to strip that part out entirely, since it's giving a lot of problems, or maybe figure out a way to delineate when a surface is loaded but a player isn't being placed on the surface itself (in the scenario you described). The hard part for me personally is that I don't use any of the mods that use new/different surfaces so it's going to be a bit more difficult for me to test what the effects are of a particular change. I will take another stab this weekend at stripping out that function so the mod is at least stable.
I appreciate your patience with me! Full transparency, I lost a bunch of work that was supposed to go into 1.3.3 originally, so I've been pretty bummed/avoiding Factorio because of that, but I will make every effort to at least get you all stabilized so you can continue enjoying the mod while I pout.
On the SE integration side, I don't have the code in a repo yet but I'll get that setup this weekend too and if you're comfortable you can make a pull request with the SE changes. I'll let you know when that's ready.