We used to drop a weight line from the tibial tuberosity once the saddle height was correct and at the same time set the cleats so that the ball of the foot and the drop weight were directly over the pedal axle. Now we have charts and formulas to help us get in that ballpark. Multiple stems together with multiple setback seat posts introduce more than 1 variable to the rest of the calculation. Using variably different setback seat posts would again be like moving a saddle fore and aft on its rails to solve a reach problem.
Yes, use whatever saddle and seat post gets you correctly over the drive of the bicycle and then worry whether your top tube and stem will take care of the rest.