b2z Stef_ I've seen this complaint come up a few times before, and I think the language clarity is an issue. Flarum seems to categorize tags in two ways when there are three. There are Primary tags, (what I call) Nested Secondary tags, and Secondary tags (luceos here calls those Helper tags, but those are just how we use them here on discuss). But the language inside the Admin panel seems to conflate the Nested Secondary tags with Primary tags, even though the code itself treats Nested Secondaries and Secondaries (standalone) the same.
I think it's a mild bug, and a confusion that needs correcting first at the language level, and then we should look at whether the behavior reflects what Flarum wants to happen.
Your use case seems perfectly valid, the question is really about whether that's something Flarum wants to offer in core or just allow a community extension to be written. There are certainly plenty of avenues where the Tags extension could be extended in ways that would help certain communities, this is definitely one such case.