Hi,
The name of 'Multi-Tenant Migrations' has caused some confusion - we've actually recently renamed the new feature to 'Multiple Contexts per Database' to help make it clearer what scenario we are targeting with that feature.
That said, your scenario is an important one and is tracked by this issue - http://entityframework.codeplex.com/workitem/54. I don't think we're going to be able to do much to improve it in EF6 (we're working on our last few features and then we're focusing on improving quality to get ready to RTM) . However, introducing DbModelBuilder.HasDefaultSchema will have made things a bit easier if you are separating by schema. I'm pretty sure you can get migrations to work in this scenario... but it would require some conditional code in the migrations code files. I'll play around with it and publish a new blog post :)
~Rowan