Same here...
You can hide it with a right click, but, like you I would want a proper solution.
Same here as well, I opted out of beta program but see the 10.12.1 beta update.
I even re-enrolled my Mac in Beta Program then opted out again, no change.
I also reset my local App Store cache ( ~/Library/Caches/com.apple.appstore ) with no change.
I hope this doesn't mean we won't see the non 10.12.1 final release or any non-beta updates that happen in the meantime. Maybe 10.12.1 will fix this going forward.
I just reported this to
http://www.apple.com/feedback/macosx.html and referenced this thread, so anyone else who is having this problem please speak up and also send Apple a report.