I agree with you to an extent. There is a consistency with the Apple UI, given that its sandboxed nature dictates the location of application settings. Doesn't make it less frustrating to use, for sure.
Because Android is an open source OS, even if it is owned by Google, and telling the vendors how to build the devices would probably go against the agreements set in place by the OHA. Design guidelines being controlled in house are far easier to manage and execute than dictating to your vendors as to how they can build their devices, in any event.
On top of it- the different vendors use the buttons for different reasons, because of their own overlying UI (eg how Sense 5 uses a different layout to Touchwiz). The best way to unify the way Android should ideally look, is for Google to present that themselves.
The Ubuntu Touch UI, is probably the best executed that I have seen, with its use of swipes- it is fluid and really shows you that buttons are legacy components. WebOS too, had this done well. Android is still a bit broken in this aspect (menu keys in most apps, but swipe gestures for certain features).
And ultimately, touchscreen is not only the most reliable, but the most consistent experience. Having buttons sort of takes away the overall purpose of a touchscreen, and creates a slightly broken user experience. Having all the functionality available from a single input is the ideal, I would wager.
I agree in principle, that the risk is there. But I have never hit it accidentally. I have, though, hit the physical back button accidentally whilst holding the device a certain way. You could argue that it's crap design to have a physical button on the bezel as you risk hitting it while using the device in landscape mode, or that it takes away from a unified look on the front of the device.
On screen keys are functionally superior, more reliable and with KitKat, not a screen reducing aspect anymore. The only thing that hardware buttons offer over them would be the tactile feel of actually pressing a key. But, this was the same "problem" thrown at early touch screen devices. Eventually, we got over that one...
BTW- I'm not dismissing your opinion. Hardware keys can be and are useful to those that prefer them. But from a design, functionality and UI flow perspective, on screen keys trump them in all aspects, especially now that the OS now makes provision for the loss of screen estate that they initially took up.