The bay area is more than SF. If you mean San Francisco and don't want to say the whole name, you use either 'SF' or 'the city.'

I'm not sure why it's a strange shibboleth? Not every name has to be shortened, and if you are going to shorten names, not every short form is acceptable. I don't know where "San Fran" came from, any more than "Cali", neither of which are used by locals, but it just doesn't feel respectable. It's not the name of the city.