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I'm not clear how this is related to Flask-SQLAlchemy, or the scope of its docs. Marshmallow-SQLAlchemy, which is I think what you're referring to when you say "schema" is a completely separate project. Additionally, everything you said seems to apply to SQLAlchemy in general, not anything Flask or Flask-SQLAlchemy does.
EDIT: This isn't related to Flask-SQLAlchemy, see here for related issue:
marshmallow-code/flask-marshmallow#143
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