I recognize there is a need to distinguish between comments for the developers (e.g. FIXME: foo bar) and comments for the users (literate programming style), however I think there is sometimes a need to extract comments out from places other than top-level comments and doc-strings from (mostly) top-level forms.
For example, I'm experimenting with writing a CAS server in Clojure that structurally mirrors the CAS protocol spec. Ideally, I'd run this through marginalia, but unfortunately because I want protocol spec sections to be close to the defining code, the comments sometimes lay internal to outer forms.
My suggestion would be to allow "heavy" comments to sink to the left and become marginalia text. To make comments heavy, perhaps we use ;;; or ;;;; to distinguish them from in-line code comments.
I just saw the inner comments branch. I'll give that a try...