I agree with most of what you're saying. Add To Homescreen is a great feature for regular users of a mobile web app. Your application needs to support both modes however (browser-mode, and app-mode). The easy answer is to say: "Use back button in browser, and use navigation bar in app-mode" - Which is certainly possible from a technical perspective, but jarring from a UX perspective. You have to essentially re-learn how to use the application when you click that button. Not only that, but if you add a navigation bar in app-mode, then your navigation is on the top (where it would've been on the bottom in browser mode), and that has other fallout in relation to other elements that you may have placed on the top of the page in browser-mode.

I hope that made sense.