Yeah, the last 5 jobs (of 6 jobs) I've had I've applied with a markdown file or just a link to the rendered webpage in an email, IIRC.
In my head at least, it helps me filter for companies/managers that appreciate a hacker mentality. I also suspect it might help the applicant tracking systems parse my shit more correctly since it's just plaintext. (Though the opposite could also be true since I assume the vast majority of submissions would be PDF.)