Just to followup on my post, through trial and error I am now able to sometimes launch from pads on other bodies. However, it's definitely fiddly. Sometimes I have to try the same launch three or four times, or switch pads a few times, etc. before it works. I'm currently under the impression that it's one launch behind - in other words, I have to launch with Mun 1 selected, then recover (not revert!) since the craft will be on the Kerbin pad, then launch again with Mun 1 selected, and then it will work. But even this process is not 100% reliable. I'll keep you posted if I can narrow it down further.
In any case, thanks for all your work building and maintaining this mod. It's become indispensable for these 7000 ton Minmus launches I keep wanting to do