"I've frequently wondered why a hierarchical approach is the norm for text formatting."
80/20, if not 90/10, effectiveness. Most people are not trying to do what the Wikipedia article is talking about. About the most complicated thing that people want to do is the moral equivalent of <i>italic <b>bold and italic</i> bold</b>, and you can losslessly convert that to <i>italic <b>bold and italic</b></i><b> bold</b> for almost all practical purposes.
It isn't until you're getting very precise about what your tags mean, for tags that intrinsically "cross" hierarchies like that, that you start seeing this issues. And then by the time you've gotten that far, you realize you have all sorts of problems, as the article says.
But a good deal of the answer is that while the stuff mentioned in the Wikipedia article is true and important, it's also fairly specialist.
As for "The only place I've seen this in practice is in Telegram's TL Schema [1]. Is this method found anywhere else?", tag-based formatting is the norm for rich text widgets, which generally can natively represent my first HTML example above in its internal format. Generally if you dig into your favorite language you'll find someone has already implemented this efficiently as a library you can pick up if you want to use the capability directly outside of a text widget. It has its own consequences, as anyone who has ever fought with them may realize, but it's not impossibly difficult to deal with.
It isn't a magic solution to everything either, though. Even if it is what you think you want, a widget able to represent a bold section starting in the middle of a paragraph, then proceeding through the first three rows of a table, then stopping in the middle of a paragraph in the third column of the next row is generally weird. To some extent, people have a certain hierarchiness to their thinking about these matters too, whether it's cause or effect. But that hierarchiness is messy; I think it's fair to say most people wouldn't "mean" that bold to mean something in my table case, we don't necessarily expect tags to proceed through tables like that, but <i>i<b>bi</i>b</b> is something that people might intuitively expect to be able to do. It's a fractally messy space both in the computer science and human expectations, and the fractal messiness only gets messier when we try to harmonize those two things.