It's not too hard, I adapted Ian Hill's Soda (which clearly was also used for a lot of the UI in this theme) to Solarized for the same reason here: https://github.com/jrolfs/sodarized. I'd be happy to answer any questions about doing so for base16.
I've looked into this a bit. I don't think it's just Chrome but rather YouTube has some sort of beta flag for enabling the pjax style page loads. Try Incognito in Chrome and see if you still get the bar.