... which is what iTunes does

If it were to be changed to three buttons, then I suppose the options to "Would you like to apply the changes?" should be " Yes | No | Cancel" where Yes would apply the changes, no would 'discard' them and continue moving away, while Cancel would leave you there to continue editing.

Lol, perhaps I've just been corrupted by iTunes that uses contrary terminology.

I'd still like to see 3 buttons

1. Applies the settings
2. Discards the settings
3. Reverts to the settings page to allow further modification

The third option isn't available at present.

It's not asking if you want to "(cancel) your navigation away" though. It's asking if you want to "(cancel) your changes." I see nothing wrong here.

Very minor point ...

When a device's auto sync list has been changed and you don't click "Apply" before navigating away from the tree node there is a prompt which says: "You have changed the settings for xxxxxx. Would you like to apply these changes?" and you are given "Apply" and "Cancel" buttons.

"Apply" applies the settings as you would expect.
"Cancel" does not cancel the navigation away from the node but actually discards the changes.

I think buttons should be renamed "Apply" and "Discard".

Additionally I'd like to see a new "Cancel" button that cancels the navigation movement any takes you back to the device configuration page.