If you can get the same saddle height and setback on a 52cm frame and a 54cm frame then its the same, but remember that this is all being measured from the centre of the BB.
Smaller frames next to always have a steeper seat tube angle (they shouldn't yet it a common fudge) so the saddle starts out with less saddle setback and in order to get it in the same position as a larger frame(with a more relaxed seat tube angle) you will need a seatpost with more setback and/or set the seat further back on the rails.
How have you measured saddle setback?
This measurement is once again, measured from the centre of the BB and it takes a deliberate effort to get it the same on different bikes.
EDIT: If the seat and handlebar positions on two seperate bikes is indeed exactly the same in relation to the BB, then you really should balance exactly the same on both bikes. How you balance over the wheels however will differ and this is ONE factor that will effect how the bike handles.
Last edited by AnthonyG; 06-04-21 at 08:05 AM.