What’s the expected behavior for muting categories + watching/tracking tags? I have a use case where a user wants to mute all untagged posts and be notified of posts with specific tags. I tried this here on Meta and I muted all categories in my preferences, then watched and tracked a few tags that I knew had recent posts, but everything still shows up in latest. Is this the expected behavior? Is there another way to hide all posts in latest except for opt-in tags?
That depends on the user’s preference for
Notify me about topics in categories or tags I’m watching that also belong to one I have muted
It’s a little hidden, but you can see it when you are watching at least one category and mute at least one tag:
Then you can change it, save and adjust your tracking preferences again.
Admins can also configure a default for it in the site settings.
What I often forget while testing is that the tracking levels of existing topics are often no longer based on the category/tag default, but are influenced by auto tracking based on reading and replying.
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What about the reverse though – what I’m trying to figure out is the behavior of watched or tracked tags in a muted category? What you’ve got in your screenshot is watched category with a muted tag. I don’t get a similar “Notify me” check box when I have categories muted but a tag watched.
I think that is a bug in the code which is responsible to show this setting. I think it should always be visible, but it’s hidden if there is no watched category 
That’s why I said that you need to add a category to watching to be able to see the setting. Once it’s changed, you can configure the category notification levels as you like. It’s only the interface that hides the checkbox. The value is still stored.