it would require meddling with the Hubski's markup engine, no?
It would require setting up additional markup, yes. Considering Hubski already having custom markup system (there's no other place that uses plus symbols for embolding the text), it shouldn't be a problem.
I suggest something simple using parentheses. For example,
(! comment to be displayed as margin note)
(1 comment to be displayed as sidenote, enumerated automatically)
Not sure if it would work as well with comments as it does with posts.
Preliminary thinking says the comments could have inline note in separate paragraphs aligned the opposite of the main text (to the right if you're anywhere other than the Arab or Israeli states). Also possible to shorten the comments themselves to, let's say, 400px (which is me eyeballing it to be 50 to 60 symbols at current font size, giving it the optimal reading performance), which would give sidenotes and margin notes some space.