The top tubes are actually relatively long: 59cm on the Raleigh (not vintage), 59cm on the Centurion (from 1984), and a whopping 63cm on the Schwinn (from 1980). I'm using 130mm stems on the Raleigh and Centurion and 90mm on the Schwinn.

These are normal-to-long top tube lengths for large road frames. My guess is that the top tubes look shorter because large-framed bikes look weird to begin with, a sort of optical illusion but more because it's a comparison of a normal-looking bike (the 54-58cm bikes that are by far the most common, in the middle range of sizes) with 63cm and larger frames.

Seat setback is irrelevant here because knees coming close to bumping the bar-ends happens only when standing up. So the principle distance that matters is horizontal distance between the crank and the handlebars.

Anyway, I'm not sure what the ideal parameters of fit should be here. With the bars way low on the Raleigh (and subsequently at least 1cm further forward than on the Centurion) I don't hit my knees. With a Rivendell setup where the bars are high up but proportionally further ahead horizontally from the saddle, people don't have many problems. Maybe my Centurion is just in the middle and it doesn't work as well.

And again, I don't hit my knees on the bar-ends of the Centurion. They're 44cm wide. But I come closer than I'd like.