I'm 5'6" and have a 52cm Specialized Allez. Another shop did some measurements and said I should have a 54cm frame. Since the Allez top tube is arched, is 52cm the best choice. And does 2cm even make a difference?

Yes, size makes a difference, but I'm not sure top tube shape makes a difference. I'm 66.5". I have a 50, a 52, and a 54, all with level top tubes. The 50 is a bit small, the 52 has a fairly long top tube and the 54 a fairly short top tube. They all work. The 54 has only a couple inches of seatpost visible. The 52 has more drop to the bars.

I put a lot of mileage on 59 and 61 cm Lemond bikes. Without adjustments, the 59 was on the cusp of being too small and the 61 was too big. With adjustments, both were great bikes.

The arch in the top tube is only an issue on the larger bike if you have really short legs for your height. 54cnm is really on the cusp of being too big for 5'6", unless you have extraordinarily long arms and legs. Especially for Specialized road bikes, which run large for their nominal size. If you're feeling cramped on your 52, look into a longer stem and a little more saddle setback.

Yes. I ride 54,55,56,& 58. They are all cheated to fit to some extent, but beyond the fact that they are different frames there is subtle difference in riding style. My experience is smaller bikes tend to move your weight forward and put more emphasis on firing quad muscles.