That may well be overengineering the solution. I think it'd be fine to configure_file the desktop file and build the list of miemtypes programmatically at build time and let packagers override it.
Separate mimetype files would only be useful if platform 'foo' has >1 packagekit backend and the list of supported formats is different between the backends. Which I think is not the case for any right now.

That being said, should it become necessary, separate files would be the way to go.
For packagers this is then representable as

• pk-backend-foo --(depends)--> discover-backend-foo [only contains desktop file]
• pk-backend-bar --(depends)--> discover-backend-bar [only contains desktop file]