As someone who also made the jump from primarily using PHP to Python a while back, I have to say that a lot of this is very trivial stuff.
Maybe my experience was different because I was already heavily using ORM's (SilverStripe in particular) to build complex apps very rapidly, and moving to Python+Django was a far more natural process.
> "the fact that Django makes most of the decisions about how the database will be structured just baffled me"
You define your structure with your model, so this is baffling to me. If you're worried about trivialities like column or table names, you're worried about the wrong things.
Anyway, I think that a bit of time with Django and you'll never want to go back. I certainly don't.