How are you doing meaning-aware pagination if you're zipping together markdown columns?

A few minutes of asking an AI and writing a pair of simple typst docs with a few sections of #lorem() paragraphs resulted in what I think your ad-hoc scripting (in what language? add and your custom scripting to your collaborators' publishing stack) efforts do: a typst meta-document that pairs two simpler typst documents, section by section, paragraph by paragraph, each sub-document with its own column width and font size, paginated on paragraph breaks. You might balk at typst's embedded language, but it does avoid added dependencies and external scripting, and the language looks fairly simple a nice and functional.

It might require a somewhat different design to accommodate a marginal-note kind of thing with irregular vertical spacing not paragraph-aligned, but I suspect that's quite possible too, probably with some markup to label notes and align them vertically with corresponding labels in the primary text.