When the touch screen is used as a replacement for physical buttons - to answer or ignore a call, for example then using the screen is roughly equivalent to having a capacitive button for the same function.
Except the iPhone was damned clever in that regard. It has a proximity sensor next to the earpiece that would shut off the display. So, as soon as you go to answer a call, the phone detects your ear and shuts off the display so you don't accidentally do something stupid with your cheek.
Only very, very roughly. The issue is dedicated capacitive buttons. On-screen buttons can give visual feedback, and are only present when they are contextually appropriate. Capacitive buttons are dedicated spots on the hardware that are always present no matter what you are using your device for at the moment.
Yes, it's an important distinction. Still, there are valid reasons for preferring physical buttons that virtual buttons or other on-screen controls do not address.
1. Feedback. This turns out to not be important for most people for most tasks. Still physical feedback (of layout and of action) important tool of physical interaction and required for eyes-free operation. I fully expect this problem to be solved within two years.
2. Software bypass. This is mostly useful in case of complete software lockup (low level/OS crash), but while most phones are built to be "always on" you can't always avoid low-level lock-up. And in that case you need to reset all transient device state. I expect the final fail-safe to remain a physical button, although some kind of watchdog running alongside the OS itself may be able to take care of 99% of the lockups.
I was going to say tactile positioning, but you seem to be rolling that in to feedback/layout. I would also add the distinction between putting your finger on a control and actually activating it. Capacitive technology doesn't provide a good way to handle that[0]. For an extreme example of the type of control you'd like to make such a distinction, consider the trigger of a gun. It may be important to be very ready to activate the control, and even more important to not activate it prematurely.
[0] I don't consider press and hold, double-tap or similar to be good general-purpose solutions to this
