Installed 16299.15 RS3 on test machine.
Three notification settings cannot be disabled. Turn them off, and they just turn back on again.
(Notifications from Apps and other senders, notifications on lock screen and notifications about VOIP calls).
Turned them off, and went into group policy editor and disabled the notifications under user configuration. But of course that does not work because even though the slider moved to "Off" the settings are not actually being turned off.

Does anyone know of a fix?

Know the specific registry keys for these three settings? - If I set them off, assuming it's not Microsoft deliberately defaulting them to "ON" wouldn't that work?