> The problem is that in most cases where I have to use markdown, it's not a source file. E.g. if in a git comment I use a single newline to separate some points, it's often a surprise to then find them concatenated on a single line.

Git commit messages (I assume that's what you mean by comment) are conventionally fill-paragraph'd with the traditional 72/80 limit, so I would expect this reformatting to occur. Markdown has proper bulleted list supports, use that. Or paragraphs. It also supports explicit linebreaks (two trailing spaces) but that's usually hard to read.

> Like this very hacker news comment box here. I know it's not really markdown, but it also ignores single newlines. Why?

Well in no small part because it blows chunks.

> But markdown is for writing natural language, isn't it a nightmare then to keep all lines 80 characters if you edit previous sentences or insert a word somewhere?

1. markdown (and most other lightweight markups) grew from email conventions and conventionally formatted text files (check out the text RFCs)

2. in emacs, re-filling a paragraph is an M-q away