So it appears to be not elixir proper, but some people's overrides of flycheck-elixir? I'm going to do the research a bit more carefully now and write it up for Kakoune.

I think I've been misunderstanding something... the buffer default-directory isn't really buffer-specific, and it's just emacs current working directory?

Okay, it is buffer specific, but it isn't the immediate ancestor of the buffer's file.

if I log the current working directory to a file in clj-kondo, I do get the parent directory of the buffer's file