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By the way, in case anyone needed to know this, there's literally a book next to the link section that just lets you make citations automatically and it's the easiest thing in the motherfuckin marvel 3 editor. You can even make citations to earlier citations. Doing that manually is a nightmare, so this should make it easier for everyone.
You still need to do the actual citing part yourself obviously, tho.
I tested it out myself. It handles references used several times in a single page fairly cleanly (it gives them different dummy names, first one is named ":0").
While it does preserve issues and weirdness from other parts of the visual editor (trying to add links in references causes the same issues adding links anywhere in visual editor does), the references portion itself doesn't seem to cause formatting issues.