I think that an "ignore hardware configuration from snapshots" option would be a really nice addition.
Not only it would avoid the annoyingness of having your config changed to oftentimes-unwanted values but also make it possible to do things like enabling the AY sound by loading certain Z80 files while the current machine is a 128K model (examples include many Opera Soft games such as Goody or Mutan Zone).
Real hardware already does this when loading through a DivIDE (for obvious physical reasons) so I guess it would kind of make the emulator more accurate, too?