I am late to the game, but I wanted to put my voice in as one of those people who cannot stand over their bikes completely (my crotch touches the top tube of both) but my bikes fit me very well. Since you don't get on your bicycle by sitting on the seat and then pedaling off into the distance, I don't think that it really matters. I get on my platform pedal bike the same as I do the clipless - right foot slightly raised and resting on the pedal, bike leaned slightly towards me, push down on right pedal while lifting body off ground, sit down, connect left foot to pedal; get off in reverse order.

What DOES matter is you foot position on your pedals and thus your butt's distance from the end of the crank arm. I'm not sure if your heel should touch the pedals, but definitely the ball of your foot should (my heel does not touch my pedals). When you are at the bottom of the pedal stroke, with the ball of your foot on the pedal, your knee should be at approximately a 20˚ bend (I think that's the correct one). This is where you get maximum power and you aren't damaging your knees internal structure. You can measure and adjust your bike yourself to get to this level - I was professionally fitted on one bike and now I go from those baselines and tinker with my bikes myself. However, you did pay for a fitting and so I would definitely be upset if I were you.

The last thing I might mention is - even with all the numbers in the world, a "perfect" fitting may still not actually fit you. You are you - not some numbers - and if you are still uncomfortable on the bike, you aren't fit properly. It's just like in medicine - the lab can give you all kinds of numbers from the blood, but you have to look at the patient, not the numbers, to get a true picture of what's going on. Have them fit you again, on this bike, and don't leave until you are really comfortable.