This is only if you use it hierarchically. No one prevents you from having a tag projects and another tag newproject. Your emails just have both tags assigned and you are good to go

Sure, but GP's point (and it's something that annoyed me in Fastmail too) is that if you do have an 'hierarchical tag' - which could be in addition to unrelated tags - you don't get the '<sub-tag> is a <super-tag>' that you might expect.

The tags themselves end up in an hierarchy without it affecting the tagged contents.

From a document perspective, yes, you're correct.

From a tagest perspective, and the discovery affordances, there is a significant difference.

Hierarchical tagsets allow you to navigate via tags, affording document discovery by that mechanism.

That becomes more significant as you're working with a larger, richer, and more structured tagset.

I think what you're seeing is the opposite: tags aren't hierarchical. Tags can be organized hierarchically, for organizational purposes, and you can use rules to ensure that everything tagged "projects-FOO" is also tagged "projects", but the tags as they apply to tagged objects aren't hierarchical.