The angles are different. A 52cm + 54cm frame may be a 'M', or a 54cm + 56cm may be a 'M' - either way, you're taking two frame sizes and adjusting the angles for a "better all-around fit". If someone really rides a 52cm, and is on a 'M', angles such as ST and HT are different, while apparently "maintaining" an equivalent TT length. Often times, you're also combining sizes, so the hub will not be completely blocked out. It's merely giving the "equivalent" TT length in that size.

Fit will come down to feel and preference. I had a Trek 2500 with a setback seatpost and 90mm stem, I moved to a 0-setback post and 110mm stem (keeping the same overall length) and found it far more comfortable.