Web API in Flask
I'm not sure what you mean by
If I define all my objects at module level, I have no way to interact with them afterwards, do I?
But no, you don't have to define your objects at the module level - that's true of your Flask instance, blueprints and any object which you provide. For example you can create an AppBuilder class that makes and configures Flask instances.
For some interactions context locals are a very handy tool as well.
If you can clarify the issue I'll try to expand my answer.