Depending on the rider's physical proportions, mass distribution and intended pedaling intensity, the positioning of the saddle and handlebar relative to the bb can be all over the place.

Shorter, more-intense rides with very-fit riders favor a body mass center that is further ahead of the bottom bracket, the better to resist pedaling forces which apply rearward rotation torque about the bb to the rider's body.

And such forward positioning of the rider over the bb will move the rider's hands both forward and downward along a circle centered around the bb.

So, for better mass-balance over the bb while pedaling hard, a lower and longer stem becomes appropriate as the saddle also moves forward.
Endurance bikes favor a more-rearward body mass positioning over the bb as appropriate to a lower level of pedaling force.
So with that, a taller headtube allows the handlebar position to follow the concentric circle about the bb upward and rearward as the saddle moves rearward.

A bigger frame can tend to force the issue toward a forward body positioning, as the rider tries to achieve a better mass positioning over the bb so as to prevent the steering from feeling too flighty if it's a race bike with aggressive steering geometry.
Using a shorter stem not only quickens the steering, but also puts the front tire further ahead of the rider's body and closer to a leading rider's rear wheel, so drafting efficiency is compromised.

This one is a good visual example of my trying to fit on a bike with a bit too much toptube length for all but very intense levels of pedaling effort relative to my age. Thus descending comfort and control are likely compromised, as is comfort on longer rides. Still not a bad bike for 2-3-hour rides however, and I'll perhaps try a shorter stem one of these days if I don't sell it first.