There are quite a few things that will stop any sort of structured output in that sample:
None of your headings are going to be useable for any markdown output:
[code]
::: {custom-style="Outline Chapter Title"} :::
Chapter One: # Introduction #
:::[/code]
The octothorpe # is lost in the prefix, therefore pandoc/mmd cannot parse it as a title. Headings need to be on a line by themselves, with the octothorpe the first character. Also, custom styles will not be applied in this case (as the heading supercedes the custom block), you need to use another format for headings, or better yet just use the default heading styles.
Your compile settings don’t convert Scrivener links to multimarkdown, thus they will not be clickable.
Currently there is a bug in Scrivener that you will hit once you fix the other problems: https://forum.literatureandlatte.com/t/markdown-titles-and-prefixed-document-links/48664/1 — basically even if you remove all your styling the links will become:
... in Chapter [3](#3 Blue)...
Note the # which is not in the actual title. Scrivener will also copy markdown into the title, so for example you cannot use inline styles (currently you use STRONG for some of your title styles), as you end up with:
... in Chapter [3](#3 **Blue**)...
The asterisks will be removed by pandoc in the title, but not the link, causing links to break…
My general feeling is you are trying to do way too much with that Scrivener compile format, layering on section formatting prefix/suffix on top of paragraph and character styles. This produces invalid markdown, and I think there is no way Scrivener or Pandoc can cleanly resolve cross references…
