"Conrad credits his 'incredible engineering team' for pulling off this transition from Flash dependance to HTML5. And while it’s clear that the Flash addiction has been kicked, Conrad notes that they continue to have fall-back Flash elements for browsers not fully HTML5-compliant."
Honestly, even if they still used Flash to play music and did the rest in HTML it would still be a huge improvement.
See Froiveshark's cowpewter comment here which goes into better detail about why they did what they did: http://news.ycombinator.com/item?id=1968668
The whole point of HTML5 tags like <audio> are to make content completely open. Unfortunately, that's the exact opposite of what what any major record label wants. I'm pretty sure they'll use flash in the background to play the audio, even if the entire site all the way down to the progress bar are HTML5.