Well, for one, if you knew as much as you say you do about SF you would know nobody calls it "San Fran".
In Vancouver, Canada, we call it "San Fran", as well. I don't know anybody there that would even recognise it if it was called "Frisco" much less "The Bay (Area)", unless more context was given.
In my group of east-coast friends and family:
Under 50ish: it's San Fran Over: Frisco
Locally? Bay Area. The City. Etc.