Whether or not it's intended to be a hidden source format, the fact remains that
if it does not render reliably and repeatably, it's failing to do its job.
Markdown's job is to be a human-readable, lightweight, unobtrusive way of communicating to software how to structure and format a document.
It's one thing for a freshly-entered document to fail -- errors in markup occur and need to be corrected. It's another to change the behaviour and output of an unchanged text, which is what Markdown implementations have done.
(I've run into this myself on Ello where, For Mysterious and Diverse Reasons, posts and comments which I'd previously entered change their rendering even when I've not touched the content myself. This is compounded by an idiotic editor which literally won't not muck with plain ASCII text entered and insists on inserting or creating hidden characters or control codes. Among the reasons for my eventual disenchantement of what would otherwise be an excellent long-form text-publishing platform.)