Looks like in CU4 of SFB 2015 new settings are introduced with platform wide scope. You can see these through command.
It also has a parameter for Push notifications.
If you are observing that client is registering to Push notification services even though you have disabled Push notifications in PushNotificationConfiguration.
On the Client side you may see below in logs,
2018-01-04 18:41:36.332 00000001b6493b80 INFO UI SFBApnsPushNotificationsManager.m:52 VoIP APNS push registration initiated.^M
2018-01-04 18:41:36.757 00000001b6493b80 INFO UI SFBApnsPushNotificationsManager.m:62 VoIP push registration succeeded.
It seems like settings in Platform level triggers and act as global settings as well. Which cause clients to see Pushnotification is enabled.
Incase you want to disable Push Notifications it needs to be disabled at Platform level using command.
Set-CsPlatformServiceSettings -EnablePushNotifications $False