1) From a UX perspective, we prefer to have the majority of the UI within a tab. We don't want to build up an entirely separate UI hierarchy outside tabs.
2) We tried putting native UI within a tab in early versions of Chrome, and it did not feel right. There was an uncanny valley effect. If the content of a tab doesn't feel like HTML, it feels wrong. And it isn't practical to emulate the feel of HTML perfectly with native code.
3) The Chrome team puts a lot of engineering effort into making the web platform as strong as it can be. We would like to eat our own dogfood when possible.
I don't understand why on (chrome://chrome/settings/) I have blue links, blue underlined links, and buttons. I guess I could figure it out, but the meaning is opaque to me at the moment.
I mean, this is standard advice for web apps and services, right? You build the control interface completely outside the main user app.