Well one, thanks for alembic and SQLalchemy :) Two, this issue does seem very important.
I'm exploring options at work (essentially SQLAlchemy vs Alembic) and this issue caused me to drop Alembic. I'm glad I found the work around and would suggest that it be placed in the tutorial. I'd imagine 99% of people want to use more than one object with alembic.
I'm a bit confused now. Because I tried with one of my models, and autogenerated against a blank sql database and it generated (seemingly) all the tables and columns I would need, even ones it has no relation too.
Maybe it's the structure of the app I've inherited, and also my own confusion. Do we actually need to supply multiple metadata?