I do enough front-end to understand why Youtube does what it does. I don't do enough to think that every site implementing its own way to reload parts of pages is a sane idea.
The beautiful thing is that the progress bar in question comes from one of the companies that pioneered lack of a progress bar in the browser. But hey, Javascript.
Google pioneered a minimal browser that left most things up to the sites inside it. Seems to have worked out for them.
If Youtube finds that a progress bar is good for their user experience, more power to them. They can make sure it works as well as possible with their site, and change and remove it if necessary. It seems that you know more about Youtube's design than Youtube's designers.
Next up: have browsers ignore hyperlinks, Youtube designers can come up with a beautiful way to represent and interpret intent to navigate to a different resource and delight users - and change and remove it if necessary
The beautiful thing is that the progress bar in question comes from one of the companies that pioneered lack of a progress bar in the browser. But hey, Javascript.