I am not sure it actually is a glitch. Or at least if it is a glitch, it one that seems to make sense on its own terms.
To me, a nsfw tag that is the primary tag (the one that determines the URL) indicates that the primary focus of the content is the NSFW aspect.
Something like sexy santa, or photography that incorporates some nudity, OTOH even though there is a NSFW aspect to it, the NSFW aspect is incidental to the post.
So basically the difference between art and porn. ANd before you ask, i determine the difference the same way potter stewart did.
the solution you mention in your last paragraph seems reasonable to me.
That said, the "issue" with people that elect to downvote this material is an issue with the site as well, and the entirely fictional representation of the downvote as a flag.
What you said about it being the intended behavior makes sense. It could be that way by design. I am hoping the change to allow each user to filter for whether or not they want to see that type of content goes through. It seems like a good compromise that would make both sides happy.