, it's a known bug, it's fixed for the next update.
Since it's a single mesh with a single .cfg file it's a bit tricky, but your suggestion led to a Gordian solution
. At first I tried with several copies of .sm and .cfg files. Unfortunately even having docks with different names in every mesh does not fix the window problem, and with reason, from a coding point of view.
So I exported a 6-dock passenger .sm mesh from the editor, in hexagonal configuration, then I added docks manually to the relative .cfg file, Docking window sees an additional docking list, in the end it works as intended.