Actually - forget I said that ;). There's no problem in the migration, I just got mixed up looking at Hg revision logs.
What you'll see is that the Create method runs all the migrations needed, and returns 3 - indicating the database is up to the latest revision.
However for an upgrading user, they will instead get UpdateFrom1() and UpdateFrom2() for an upgrade path to the same latest revision.
It's just so there's only a single install step for a new installation.