Re. Markdown source view: specifying width in terms of number of characters works perfectly well with proportional fonts. It may take more tinkering to get the view that the user wants, but once set it’s not going to be changed much, if at all.
Ulysses, for instance, allows the use of monospace or proportional fonts but only provides the ability to set width in characters.
Setting a default width in RTF or formatted notes is a different matter. As @chrillek said, WYSIWYG and text probably need different approaches. For WYSIWYG, can you use the RTF ruler, or a DT implementation of it that allows for defaults to be set in Prefs?