No it should NOT be handled by npm. Imagine some npm project really needs those files. Like module that is rendering markdown files to html. If npm would be that "smart" to strip your .md files, you would be pissed and blame npm. NPM is awesome as is. It's developer responsibility to write proper .npmignore, because only him/her knows what can be excluded.

Ideally people use the "files" array. It might be nice if someone writes a bot to go around and fix large packages by adding that.

What gave you a reason to believe npm was well-architected?

See my top-level comment. It should be handled by library authors, and npm does provide the tooling to do it, but most authors choose to include the files. Seems to be a difference of principle.