When Anki (Windows) displays “Collection Sync Complete”, it is rendered as a tooltip, and is an Always On Top window. As it is not a tooltip, this seems to go against Windows UI standards.
This is an asynchronous notification, so it should probably be sent to the user as a Windows notification instead.
If the devs don’t wish to use Windows notifications, then perhaps it could be changed to be displayed within the Anki window itself; for example, it could be shown as a line of text underneath the deck list, or at the bottom of the Anki window. Another option would be to temporarily change the title of the Anki window to append “Collection Sync Complete”.
(Not trying to shoot down your suggestion, but just asking)
Could you provide some other softwares which give either of the two behaviours that you are describing for a similar scenario?