One thing to remember is that the instrument should be set up for your specific preferences and playing style. Most beginners will not yet have formed preferences, so a more or less "standard" setup works fine - but as you grow as a player, you will gravitate to certain things. Personally, I am EXTREMELY picky regarding how my instruments have been set up. As a result, I typically ask that the seller do nothing more than make sure the frets are level, then I will do the rest for myself.
Again, the majority of players will not be as picky as I. But ideally the person setting up the instrument would discuss your preferences and actually watch you play before doing much of anything. One size, most definitely, does not fit all.