Agreed, new ways of ordering thoughts online is an awesome opportunity on LessWrong!
Foot notes: I’d say we already have quite a strong Roam-style organization in the hover pop-ups of LessWrong post links but as you say, it would be very nice to have a version of that for foot-notes, given their disparate nature.
Collapsible boxes: Having “fact boxes” as expandable interactive elements seems like a very good idea as well and relatively cheap to implement. I recommend looking at e.g. Hugo XML syntax for these things (XML is a pain, you can probably figure a better writing UX out).
Interactive documents: I’m more for the Obsidian thought representation but the hierarchy in Roam is quite relevant for communicating thoughts to others. I think a strong representation of this is quite relevant and might be an in-line, minimalist, recursive “collapsible box” as described above.
The shortcuts with Ctrl + Alt generally work sub-optimally for EU keyboards, I believe. Seems worth it to test alternative keyboard layouts for usability—something that most major software companies in the U.S. do not seem to do well ;-)