Top tube and stem height is determined by arm length and flexibility.  Due to the range of motion in the shoulder, we need to find a location for the stem that settles a person in an ideal angle with the least stress to the joint.  Our belief in fitting is to get the person on a bike and watch how they settle onto the bike.  At that point we can determine how the bike fits in the round.  Keep in mind when measuring between manufactures there are variances, none of which are equivalent.  Example: I had a client who rode a 60cm Trek and is on a 56 cm Specialized.  None of which add up.