I'll give it a try. Do you by any chance know if it detects different search paths too between roles? (That was my actual issue in the end while debugging why role A could execute a function and role B couldn't).
I don't have any production DBs that use public/not-instance/user-specific schemas :/
https://github.com/djrobstep/migra/blob/master/migra/migra.p...
It looks like the schema do have to have the same name between the databases, which I think is sensible but again I could be wrong. This is a darker corner of the postgres tooling world that could definitely use some light, so good on the migra devs to trying this out. If you do get it working, consider sending them a PR with some documentation on your use case!