This is a sincere question. Maybe it's obviously a bad question for some reason that's not obvious to me, but from my understanding anyway it is sincere.
One might wish that the tags applied to a given question are somewhat orthogonal from each other, because it would be a more concise way to indicate all of the different sub-topics to which a question might be relevant.
But in practice, the usefulness of tags is mostly for searching, either browsing by topic or tracking down a particular item under a particular tag you can recall (sometimes from a while ago).
Future people might want to be able to search along lots of tag lines more than wanting a question's tags to totally avoid overlap. I'm not saying that's definitely true; just that it might be true about what future people find useful and if so there would be a benefit to being able to search for something under e.g. the "elementary-set-theory" tag and the "set-theory" tag, even though seeing both on the same question now might look kind of dumb at first glance.
Of course there could be costs to tags as well. Tags presumably take up space in some database somewhere, and maybe some things the site must do to ensure performance don't scale especially well in the number of distinct tags (so consolidating highly overlapping tags then has a material benefit).
Of course there is also a cost to fixing and maintaining this. For example, a lot of time is sunk (in terms of aggregate person-minutes) into writing, reading, commenting, editing, etc., for meta posts, like this one, that work to codify exact policies surrounding all the little things that can happen when maintaining tag overlap.
Do we really know that the total up-front cost of a meta post like that will ever really be recouped in the future? How do we really know that the cost of allowing overlap of "elementary-set-theory" and "set-theory" was material enough to warrant work to edit it away (twice) and use comments to convince that tagger of the rationale, and codify what happened in meta?
I'm not trying to claim anything definitive one way or the other. But from where I am sitting, I think the site would be more useful to me if more tag overlap was allowed, even to the point where posts end up having 10+ tags, many of which are redundant (because who knows which one(s) I (or future folks) will want/need when searching later), and that the community spent roughly zero total brain cycles of current-day effort worrying about this problem. I would immediately revise my opinion if I learned there was a serious data infrastructure reason for why overlapping tags are bad, but I suspect this is very unlikely to be a meaningful bottleneck.