I’ve written my diploma thesis with Scrivener/MMD. When I remember correctly, one always HAD to have the pure LaTeX commands wrapped in HTML comments (), otherwise there would be errors when exporting.
Today, I’ve been toying around with Scrivener/MMD again. To my curiosity, I don’t get any errors when stripping the HTML comments! Did something change here or is this just pure coincidence?
Have you by any chance edited xhtml2latex.xslt to “include” clean-text-allow-latex.xslt rather than clean-text.xslt? Using latest mmd, that change passed through straight Latex for me (but also requires Latex control characters like { } $ to be managed carefully in your normal text. Without that change, I cannot get html comments to work (I believe Amber verified this).