One thing to know about Mainstage, is that is has some folders along with the project.
For sure, every project (unless it's referencing another projects' folders) has:
"Loopback and Playback" Folder
"Ultrabeat Samples" Folder
....and possibly more that I have yet to see.
If samples are missing from Mainstage, it will prompt you as to where to look.
I'm not a GarageBand user, but clearly there are differences in the kind of information that gets stored in a "Patch"
Although it likely can be done, I wouldn't recommend creating patches in GarageBand for use in MS.
....for reasons you have illustrated above.