Hi @jwielsch,
To be honest it’s even tricky for us 
Notification system is a big machine so it’s difficult to grasp all the subtilities, and since we’re actively working on it lately you’re sadely encountering some possible bad behaviours introduced by our changes.
I don’t think that assumption is right: you should have the same on the user profiles before setting allgroupimplicit to 1. I’m not even sure your problems are related to allgroupimplicit, could be a bad timing correlation. Anyway, globally the way notification settings work is the following:
- When you switch on a Notification in the global administration, you record objects in the page XWiki/Notifications/Code/NotificationAdministration
- By default the users don’t have any NotificationPreferenceClass xobjects in their profile, so when they consult their settings, by default the global settings are retrieved. Now at the very first moment they are changing a settings (switching On a notification for example) they are creating all the NotificationPreferenceClass xobject corresponding to their current setting: basically they’re not sync with the global settings anymore
So the first thing to check if you have a global problem impacting users without the NotificationPreferenceClass is XWiki/Notifications/Code/NotificationAdministration.
I don’t understand the correlation, but I don’t know about the LDAP sync mechanism in XWiki, that sounds like a bug to me: the NotificationPreferences shouldn’t be modified there. Are you sure the profiles who get the xobjects haven’t use the “clear all” button? We spotted a bug in 12.6.1 with filters and this button, could be related to that.
Sorry for all the bothering with Notification, we’ll try to release a 12.6.2 ASAP.