Solution
result = db.session.query(model.Foo1, model.Foo2)\
.join(model.Foo1, model.Foo1.id == model.Foo2.name_id)\
.filter(model.Foo1.id != 2).all()
result = db.session.query(model.Foo1, model.Foo2)\
.join(model.Foo1, model.Foo1.id == model.Foo2.name_id)\
.filter(model.Foo1.id != 2).all()