It's true, minimal-ui could be both useful and harmful, and I suppose the trade-off now has another balance, in favor of newer, bigger iPhones.
I've been dealing with the issue while working with my js framework for HTML5 apps. After many attempted solutions, each with their drawbacks, I surrendered to considering that space lost on iPhones previous than 6. Given the situation, I think that the only solid and predictable behavior is a pre-determined one.
In short, I ended up preventing any form of minimal-ui, so at least my screen height is always the same and you always know what actual space you have for your app.
With the help of time, enough users will have more room.
EDIT
This is a little simplified, for demo purpose, but should work for you. Assuming you have a main container
html, body, #main {
height: 100%;
width: 100%;
overflow: hidden;
}
.view {
width: 100%;
height: 100%;
overflow: scroll;
}
Then:
then with js, I set #main's height to the window's available height. This also helps dealing with other scrolling bugs found in both iOS and Android. It also means that you need to deal on how to update it, just note that;
I block over-scrolling when reaching the boundaries of the scroll. This one is a bit more deep in my code, but I think you can as well follow the principle of this answer for basic functionality. I think it could flickr a little, but will do the job.
As a sidenote: this app too is bookmarkable, as it uses an internal routing to hashed addresses, but I also added a prompt iOS users to add to home. I feel this way helps loyalty and returning visitors (and so the lost space is back).