You're right torso and leg lengths vary alot at times and sometimes you cannot go by std. sizing but a 48cm for you at 5'9" is way too small in my mind. I hate your LBS is one that wants that buck then throws you to the wolves!

There are some decent sizing go bys online but requires you to do some measurements. I would do a internet search and then once you find one or a few to get a cross ref. do measurements and plug them in. They should tell you then what lengths and size you would probably be best at.

Now I am just guessing here but I would say at your height you need a 54cm bike give or take. That would be a starting size for me to run with.