The proliferation of markdown forks is a mess. Can't you just use something better to begin with, like asciidoc? I think you can likely just use existing asciidoc mechanisms to support the same thing and then existing editors will still be usable.
The proliferation of markdown itself is also a mess IMO. Outside of web writing it seems really more effort than it's worth. Seems like everyone making a writing tool of any kind is ditching rich text in favor of it for no good reason.
For me, plaintext (like Markdown) is a strength over proprietary or binary formats and I've accepted the tradeoffs. It's the primary "good reason" I use Markdown. I have confidence that text will always be readable in the future even if I don't have the app that made it. Secondarily I find most word processors overkill with toolbars everywhere and I do not like using them.