I can tell that it definitely isn't using the boot_count property from Settings.Global.I think, it has to save somewhere the 10 times of the popup and only when the popup appears, it is blocked. The 10 seconds before, after restart, it works normal. Only a reset of the phone, resets the counter of the popup.
Probably there is some hidden config file that is storing the launches of com.android.phone and it can be on the /data partition or on one of /my_*