There is a lot going on in that cookie cutter. The “transaction” library for transaction management, wired into Pyramid with pyramid_tm, wired into SQLAlchemy with zope.sqlalchemy. Works nicely for Pyramid, but I don’t know how that translates to Flask.
Think on it like a middleware that wraps a transaction. It's fine, till you start consuming other Io based services (elastic/solar/...) And you find that this blocks one connection per request..
https://github.com/Pylons/pyramid-cookiecutter-starter/blob/...
I think same approach should work well for flask - just tie the session to the request object on first access.
Side note: I think we met on IRC few years ago ;-)