I would be concerned about laura*'s comment about the parts -- if they put lower grade ones that those promised, I'd be upset. It can be a mistake (when I bought mine, they put the wrong pedals, but swapped them right away after checking the original order).
Regarding the saddle position, it seems a bit high. However, in my bike, while in the saddle, I can barely put the tip of one foot on the ground, leaning the bike a bit. The key issue is how your leg is positioned while you are on the pedals, and your comfort on the bike while riding (not so much stand over height). I only tried this barefoot, by my heel does not touch the pedal at the bottom of the stroke. I cannot see it myself, but if I had to guess, I think my pedal was about 1cm away from my heel.
You could try lowering the saddle yourself (maybe as much as an inch), ride again to see how it feels. Then go to the bike shop and request a proper fit of the new bike. The reason I suggest tinkering with the saddle height yourself is that you will then "collect" more information about the fit. Else, the first thing the will do is lower the saddle and send you off. It does not sound like you connected with the right people in the bike shop (assuming that not everyone in it is obnoxious).
ETA: Re the components, if they upgraded the shifters and rear derailleur to 105 and downgraded the front derailleur and cranks, perhaps it is fair deal? I'd look up the values and I'm sure others here can provide some guidance on fairness...



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