Sorry, but I have never used a Skill script before - my tier of tool doesn't support Skill very well (OrCAD PCB Designer) anyway.
Anyway, being stubborn, I just tried an experiment - I took my board file, with just the two connectors (pads only, all lines and shapes deleted) and the board outline, and exported the remaining features to a subdrawing (clipboard file). When I imported the clipboard file into a symbol, it seems the padstacks were preserved. Next, I will try to renumber the pads, turn the board outline into a place outline, and try to place the symbol into another board. If that works, I'll report my results.
If anybody else out there has done this, please chime in - I'd like to know if there are any gotcha's.