One of the nice features, from a writer’s perspective, is that Markdown doesn’t require special markers or delimiters to start special cases. The proposal here would add this requirement to start HTML blocks or add intraword emphasis. So I think I agree with @piro_or that adding more complex (even if only a little) syntax would take away some of what makes Markdown appealing. It would reduce complexity from the spec and implementations, but seemingly at the writer’s expense.
For complex scenarios, we have the fallback to HTML. If nested emphasis is rare, HTML could be used in just those scenarios, while keeping the normal Markdown syntax simple. If the parser knows about the particular HTML tags used, they could be stored in the AST and then converted into other formats. We also have the concept of extensions, such as what GitHub have done, to use as shorter syntax in more widespread cases, such adding attributes. With these two solutions in mind (HTML fallback and extensions), other than making life easier for spec and parser writers, do we really benefit from a new set of incompatible rules?