I too always try and fix the saddle in the same position relative to the BB and to the pedal with cranks extended. Then get the handle bar height and reach to the hoods from the nose of the saddle all the same. Yet always need tweaking after a road test.
I also find it a little intriguing in the spring, when I return to my summer bike, that it never feels the same as I thought it was 6 months previously. But a few miles/days on the bike and the comfort returns.
What does confuse me is when we talk about geometry. Especially when we try hard to get the three contact points the same. The only aspects that could give a "different" ride is the fork rake and wheelbase.