The first road bike I got a few years back was a 56 (57cm top tube) and I always felt too stretched out. I later got a 54 Cannondale CAAD9 (54.5 top tube) which fit ok but ultimately I felt a little cramped even with 120 mm stem. Now I'm riding a Giant TCR M/L (57 cm top tube)with 100mm stem and it feels perfect.

My main point is different bikes fit different. A 56 is not a 56 for every make and model so you really need to get professionally fit (which you did) and get familiar with geometry measurements of specific frames you are looking at. I have had two bike with the same exact effective top tube and one felt huge and the other feels close to perfect but what I've learned is they have different angles and the head tube height is dramatically different between the two. So there are many factors in fitting a bike. If you got on the same exact bike you own now in a 54 that might force you to move the saddle back and that might effect where you are over the pedals and maybe that is why the fitter decided the 56 was a better fit.