We fit people all the time in my store using the olde timie "Fit Kit" system and my 30 + years of messing with position and fit....my (most recent) opinion is that seat tube height certainly counts to a degree but it is not the critical issue in sizing a bike.
Most people, old or young, can easily accommodate their seat tube size ranging at least an inch or a few centimeters in either direction. Obviously standover is important as the bike becomes larger for.. ahem... comfortable clearance. But to say a bike should have 1/2" or 4" clearance really doesn't say much about the bike's proper fit except in the most general and secondary sense.
That old 9" or 10 " less than inseam theory is OK, but has not much to do with ride-all-day comfort and efficiency.
Of course, if you want the stem high and the seat level with the bars (!), then a taller frame makes sense. One person's geeky look is another's Nirvana. Once it gets so high, you may as well ride an off topic bike (mountain bike.)
But in my not-so-humble opinion, the BIG deal is the top tube and stem combo measurement. Normally as stock geometry bikes get taller (larger sized) they also stretch in the top tube dimension. This can lead a disaster for that rider who wants that big bike in order to have higher bars.
I personally feel that a relatively normally configured persons (not extremely long legs or torso for their height) should have a stem in the range of 9 cm to 11.5 cm for best handling and weight distribution over the front end of the bike. If a shorter or longer stem has to be used, it compromises the "system" of bike & body. The Fit Kit system has a pretty useful chart based upon a database that proscribes a certain "cockpit" overall length (top tube + stem) that works pretty well.
Other systems use subjective decisions relative to "flexibility" and such that make it more guesswork IMO. Really good guys with years of experience (example: Ted Ernst) and a well honed eye, use none of this... They just study you on the bike and know whether you are well positioned.
Anyway, if we want the stem length to fall in this "sweet spot", it means that the top tube length has huge importance. A person who must have a 54-55 cm top tube simply could NEVER be fit properly to a bike with a 58 cm top tube. It's interesting to me that few custom & high end bike manufacturers don't want to talk about top tube lengths.
My advice? If you don't live near cycles de ORO or Ted Ernst (and other list member s who are aces at this stuff) find a long time Fit Kit trained shop or someone who has raced or ridden extensively and fit people since... 1983 at least! (see the CR time thingie applies again.) Sadly that eliminates the triathlon - fashion plate - boutique services who just got back from a fit school somewhere. I have seen some of the worst crappola fits and positions proscribed by newbies...
Greensboro, NC USA