Many typographers prefer to set lists with the text aligned on the left, and the bullets and numerals pushing into the margin, because it integrates the list better with the text and is less visually distracting. See e.g. http://www.iamdavedawson.com/articles/hanging-discussing/
If you have multiple levels of bullets, there’s usually something going wrong. Hierarchical bullet lists which use nested indents are in my experience an absolutely terrible device for conveying complicated ideas.
If you have multiple levels of bullets, there’s usually something going wrong.
Nonsense. There are many situations where 2 or even more levels of hierarchy are exactly what you want. Screwing up such a common need in favor to a questionable typographic preference is not a good idea.
And yes, in theory you can "fake" the hierarchy with headlines. In practice that tends to look rather odd and make it hard to actually recognize the hierarchy. Especially in a whitespace-heavy stylesheet like this one.
You're often right, however, the markdown spec supports nested lists, so just throwing them out (or making them far, far more difficult to understand) under the pretense that you're organizing your data poorly and should do it differently is somewhat unreasonable in this case.