No, Markdown is a format for authoring HTML. It makes a very bad interchange format because the it leaves too much ambiguity in parsing. Also, parsing speed of Markdown is much slower than the parsing speed of a strictly conforming XML file.
Parsing speed, really? In this age?
It has its problems but its easy, widely adopted, with hundreds of tools, and simply way more capable than gemtext (which is simply very bad).
Parsing Markdown is fast enough.
But I agree MD isn't a good interchange format.