I am complete baffled! I have started a new project and for a reason I cannot figure out the front matter does not render as is. I have compared the compile settings item for item with a project that renders correctly and can discover no difference.
Make sure that the Front Matter Section Type is indeed applied to your Front Matter documents.
Make sure that you haven’t applied a global font override to the whole document.
Make sure you haven’t used Styles in the Front Matter documents. (Or if you have, that those Styles are not being overridden by the Compile command.)
Could it be that the front matter folder has different textual formatting than the rest? Maybe for instance the majority of the text is double-spaced between paragraphs—which is the kind of text Markdown would prefer, with an empty line between each para—while the front matter was written single-spaced. Showing invisible characters will help you recognise the difference, if there is rich text formatting otherwise obscuring it (like single-spaced paragraphs that have a cosmetic empty space added between them).
The common result for the latter, since again Markdown doesn’t recognise paragraphs with no space between them, is for the whole section to end up as one gigantic paragraph.
Whatever the case, “as-is” does not go as deeply as you might be expecting. It will not ignore content flags like these—otherwise it would be impossible to get rid of comments and such. As-is mainly refers to how the Section Layout system works, and turns off most of what it would do.