I eventually settled on LaTeX - although I considered dropping all the way down to groff/troff and having TeX be an intermediate step in the process.
Custom LaTeX classes made this more trouble than I was willing to deal with, so I decided to not pursue it further. I suspect Markdown might have similar challenges dealing with this, although given that the "verbose mode" is just HTML, I might be able to make it work.[1]
The print media type has been around for eons, but the @page rules don't support everything I need and are generally absent in WebKit browsers.
