The “flask.ext” style of naming/importing modules has been deprecated since 2016. Here’s the reasoning. You should use the first style you described instead:
# Use this import format
from flask_sqlalchemy import SQLAlchemy
As for the suggestion that you install your flask packages globally, this somewhat defeats the purpose of using a venv in the first place. It makes it impossible to use pip freeze --local > requirements.txt to only save relevant packages, opening you up to package version conflicts.