The change I made in beta8 was just to clarify the description of the site settings - it didn’t actually change any behaviour. But still, I totally agree that separating out the behaviour would be great.
The other case to consider here is ‘publishing’ topics from a PM or from shared drafts. So I don’t think ‘with a timer’ is necessarily the best way to separate it 
Is this kind of cleanup always done via the ‘bulk’ tools? If so… perhaps we’d be better off removing the site settings and having a checkbox available on bulk actions like “skip notifications for this category change”