The Markdown in this case is more complicated than the HTML because Markdown optimizes simplicity for the overwhelmingly common case it targets (articles/content, not wrapping web page chrome). A website logo that links to the homepage is typically done in the wrapping template or even in the CSS, not in each page’s content.
HTML is sometimes more optimal for nested markup. Sometimes nesting makes Markdown hard to parse for humans or for machines, as @jgm has pointed out. But mostly only in corner cases. Mostly.
So I think the Markdown syntax complexity in this case is fine. This is not an example of a Markdown flaw.