I never said that "I don't believe you", it's just that we're mixing up some things and we don't fully understand each other (for instance Verdy_p is talking about another issue).
It's correct that it's not possible to distinguish from Special:NewMessages and email notifications/watchlisting, but it's always been like this, as well as there is a two-years old bug (which I linked from the support thread) about threads inheriting the "watched" status from their talk. The preference "Notify me by email about threads I'm watching" has never done what you say that it "plainly states", which is why I'm not sure that you remember correctly. For instance, I'm absolutely sure that on mediawiki.org, which has the same (default) settings as this wiki used to have before the recent change, not having "E-mail me on replies to a thread I am watching" enabled means that I don't receive notifications for any thread I'm watching, either directly or through its parent talk page, as it is supposed to do (however confusing it may be).
Are you really sure that you received email notifications for replies to threads you were watching outside your talk page?
Yes, I am really sure.
I am even more sure that something changed two days ago, that caused me to suddenly receive a big flood of emails, without me having changed any setting whatsoever. This is a fact.
I turned off all my email preferences and still the emails continued. Only removing the pages from my watchlist stopped them.
So apparently it is now no longer possible to watch discussion pages on the site without being flooded by emails. I would like to have that functionality restored.