Now I'm a big advocator of markdown. I use it for nearly everything, even notes of gibberish but keeping a consistent html output seems impossible.
I use tmpvar's markdown previewer to write out most things before saving it to a file, most likely to be viewed later on bitbucket or github. The problem is github and bitbucket's html style is different and by quite a bit.
Hopefully some standardisation will come from standardmarkdown.com mentioned in the article.
Right now we have the worst of both worlds. Lack of leadership from the top, and a bunch of fragmented, poorly coordinated community efforts to advance Markdown, none of which are officially canon. This isn't merely incovenient for anyone trying to find accurate information about Markdown; it's actually harming the project's future.