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Our web technology is such that we don't need to settle for a sub-par user experience that is a relic of the days where we had to serve static HTML documents one by one.

No, but the user looking at it has something better to do than watch the browser window flash white and then pop in again as the page loads and renders.

These two things are not mutually exclusive. The important things to do in this case are figuring out which part of the website is header, nav etc and not refreshing them while navigating.

It is not about performance savings, it's about the user experience. Functionality like this can be baked into websites today (basecamp-next et al), but surely it will get easier (I am thinking semantic element which already tell the browser what is a <nav>).

That's an interesting idea having the browser handle the nav persistence. I assumed it would be done with JS but I supposed when it becomes common enough having it baked into the browser would be a better idea.