I am having similar problems as you’ve stated so maybe a second post will get some more attention. I realized that the beta 2 image actually didn’t have mupen64plus installed, at least for me it didn’t seem that it was as there was no roms folder for it. Did you have a mupen64plus folder or just the n64 folder?
I tried doing a source based installation of mupen64plus but there is still no roms folder for it. I read through some of the console history and found this:
UI-Console Error: no ROM filepath given
So it seems that I should just be able to create my own folder but then I need to somehow tell mupen64plus where it is.