All of them manufacturers use different reference points for seattube height and so on, but yea your in the ballpark as far as thinking is concerned, just reference everything using the bottom bracket as the reference, your not standing on the floor when riding after all and bbs seem to be getting higher for pedal cornering clearence-raise the bb means raise the seat and raise the bars too so in the end they are all in the same position relative to each other as when you started, many modern bikes have no standover or even a defecit(tiptoes) when properly fit because of this and many new bikes are misfit due to those that cling to the old standover standby fiting method.
try this link
http://www.sheldonbrown.com/kops.html
also try this one and click on
1. Ergobike: Competition Bicycle Size/ Proportions Analysis
It's a fitting program that lets you select the bike builder.
http://www.bsn.com/Cycling/