For the email package I would be in favor of moving the tests to Lib/test. I've always found it a bit inconvenient that they are in Lib/email. After hearing of Michael's intent with unittest, and given the evolution of email5 into email5.1, I am also considering the possibility of packaging email6 (when I get to it!) as a patch set against email5, which would make this change less of an issue for email6 development.
The 2.7 sync issue is a concern, but there are certainly precedents for differing file layouts between 3.x and 2.7. I'm willing myself to deal with this for email.
Barry may have a different opinion.
All of that said, this is a general enough issue that it may be appropriate to raise it on python-dev. Even if exceptions are made for individual packages, it would be good to agree on a general "best practices" rule for this for the stdlib.