The most significant thing to me is the frame stack difference between a 54 and a 56cm model will change by 21mm, if I found the correct model/year Synapse. So if you want to get a lower bar position then you'll be able to go 21mm lower with the 54cm. However if you prefer more upright, the 56 will let you get the bars 21mm higher than the 54. Frame reach only changes by 8mm. So not a big difference and easily handled by a different length stem. Other changes are minor IMO, however the seat tube has a 30mm difference in length. So make certain the seat post of the 54cm has enough remaining in the seat tube when the saddle is set to your correct height. Which will essentially be virtually the same from the BB center on any size road bike you look at.