MiniVMac.cc only copies System, Finder and MacsBug from system disk
MiniVMac.cc is coded to copy only the System, Finder (for System ≥ 7), and MacsBug (if present) from the user-supplied system disk. What if the program the user is developing requires a system extension, control panel, preference file, or something else on the system disk? Maybe it would be better to copy everything on the user-supplied system disk (except, of course, Finder, when using System < 7, since AutoQuit will become the Finder in that case, and you can probably exclude Desktop, Desktop DB and Desktop DF as well since they'll be rebuilt). That way, the user can be in charge of setting up the system disk in whatever way is correct for their application.
What if the program the user is developing requires [...] something else on the system disk?
For example see https://github.com/autc04/Retro68/discussions/135