It's a bit of a matter of perspective.
The distinction between looking at a document in markdown versus Word is a bit analogous to the distinction between looking at a movie in its textual form as a screenplay versus looking at a movie as a piece of video: Text is capable of abstraction in a way that video is not.
In the screenplay, it might say "table", but when the director translates it to video, the director will have to decide: What kind of table? What design? What period? What texture? Is there anything on the table?
None of these decisions matter to the construction of the story, so, for a screenwriter, it would be very distracting if they had to make all of those decisions just to be able to get "table" committed to the medium.
In Markdown you worry about text and nothing but text. But Word shoves a particular font in your face as soon as you're laying down the first letter, so, if you don't like Word's choice of fonts, you can either let it annoy you throughout the project, or you can start worrying about fonts right then and there, which will be a distraction. If you write Markdown in a code editor, then, presumably, you've already set up the code editor in a way that doesn't annoy you. And then your future self (or someone else entirely) can worry about the font.