Why is a hub axle threaded so far past the bearing cones?

Not all of them are, but why not? Axle breakage isn't much of an issue anymore. And if you have to have a stress riser (threads) on a component, it's not a bad idea to just spread them evenly over the entire surface so it's dynamic characteristics remain consistent. Not sure if that's the correct engineering terminology, but whatever.

i've found good use of much of what appears to be excess threads on an axle due to rear dropout widths changing over the years. various spacing requirements have made it touch and go on a couple of my bikes and their hubs.

It's done on a Automated machine , doesn't take any more time ..

threads are rolled in (like Spokes), and then the axle is heat treated..