With Factorissimo 3 enabled, any researched factory floor surfaces will show up in the planet hopper's destination override list. Doesn't really make sense to be able to "land" in one.

These dropdown choices are not just surfaces, they are also planets (as you can tell by the missing locale key). I don't know if that's intentional, but it's the reason they would appear in the list.

As of 2.3.6, planets that mark themselves as hidden are excluded from the list.

Is it possible the hidden key isn't being respected?

I have Maraxsis, and its Trench is hidden as in, it doesn't appear on the space map. Same with the factory floors (from Factorissimo). But all of these appear in my Planet Hopper menu.

https://ibb.co/jPTjw1f5

Your screenshot actually exhibits a different bug, namely that the old override GUI from Planet Hoppers v2 is still attached to that silo. v3.0.5 cleans up the old GUI leaving just the Launch menu, which has the correct list.

Thanks a bunch :)