Besides, I ended up rolling my own migrations to have more control over things like this...
Off the top of my head, why not have a base class with the general migration pattern. Not sure how you specify the schema; Fluent NHibernate, for instance, allows Schema to be specified.
Then the tenant (schema) specific migration derives from the boilerplate code, which is also specifically versioned (somehow; again, I ended up rolling a System.Version based migration pattern).
Assuming you can isolate Schema from the boilerplate, this should be quite doable.
P.S. I wanted more control over the SQL-ness of the migration and was finding that for anything more than run-of-the-mill add a column here, drop a table there, migrations, FM wasn't quite up to it. Plus with not a lot of code, it's fairly straight forward to put EF (current versions) to work in this area.
HTH