When I read your edit before, I didn’t notice you had added this paragraph. I thought you had only revised the list, so I only read that. Sorry! This is better.
But Markdown in general has the same problem of differing support. And this paragraph and the list item before it contradict each other (if wikilinks didn’t work outside of Obsidian there would be no slightly different versions, only the one in Obsidian).
It sounds like by “natively” you mean “completely”. They’re not the same thing. Headings in wikilinks aren’t supported natively (in iA Writer, at least), but basic wikilinks are.
And while lack of support for heading and block links is a problem, it’s not specific to wikilinks. You can’t rely on heading links in Markdown because apps differ in how they convert heading text to URLs. And other apps don’t support Obsidian’s block link syntax in wikilinks or Markdown links (and the help docs point out the compatibility issue).
I didn’t say I use a flat file system; I use folders. That’s where the paths come from that I don’t want to think about when I write links. Using relative links would force me to think about them. (But people should be able to use them! So I’m disappointed by Obsidian’s poor support of them and glad mnaoumov has made it easier.)