Have tested this setup locally - and it seems to work well.
Asking for a sanity check:

One default repo.
One .thin repo.
Synching using sync and get.

The fat repo retains all the historical versions of the file.
The thin repo holds only the newest version of the file.

Can edit / sync both ways and the above two statements remain true.

Is this use case intended?
If so git-annex is brilliant =).