Edited to make this a feature request as I think it’s appropriate and will garner more discussion that way. (Note that the #developers-api section is meant for discussions among Obsidian’s community developers, not the Obsidian devs themselves.)
I think recognizing all kinds of markdown file formats is a great idea as it maximizes between-app interoperability. Like you said, even if some specific features of e.g., R don’t work in Obsidian, we should at least be able to see and look at the details of such a file from within the vault.
I believe the issue is namespace collisions. There’s a design dilemma afoot. How should Obsidian deal with two files with the same name but different file formats in a [[link]]?