Ensure GRANTED_BY_DEFAULT properly cleared in NMS

When the USER_SET flag is applied to the notification permission, or the
permission is denied, the GRANTED_BY_DEFAULT flag should be cleared.
Also fixes incorrect flag mask setting when updating permission flags

Test: atest PermissionHelperTest
Fixes: 238238487
Change-Id: Id81aef30904e38d96cef0444edc562bb2c765843