Every Markdown spec differs from others in one way or the other and there is no way to tell that if the Markdown documents I am writing today will convert to PDF, HTML, etc. in exactly the same way 10 years later as they are converting today.
Two Markdown specs may end up converting the Markdown into different types of HTML and PDF -- sometimes even with semantic changes like nested lists in one spec is broken list in another one. Nothing is more displeasing than seeing a carefully written nested lists appear as ugly code blocks within lists because a different Markdown spec does not support nested lists the same way as the first Markdown spec I was using. This is just one of many examples where Markdown for one spec can break in another spec.
If you are strictly going to stick with Hugo forever, then that's fine. But how many of us can guarantee that we want to keep using the same tool to render our Markdown for ever? I certainly can't! I really wish there was a simple documentation format that with a single spec with a large number of implementations -- something like the C89 of text formats. Is there one?