is a fenced code block meant to become a <pre><code> block?

[Southclaws]

surely it should just be <pre> I've never seen <code> nested within, now I've gotta mess around with styles that only affect a lone <code> separate from one inside a <pre>

[wooorm]

Your wrong. Every tool does this. And its in the markdown spec. The code element is for code.

[ChristianMurphy]

Welcome @Southclaws! 👋
Sorry you ran into a spot of confusion.

mdx, remark, and most markdown parsers follow CommonMark (https://commonmark.org/).
In CommonMark, fenced codeblocks include both <pre> and <code>, that is standard and there is no intent to change that as a default. https://spec.commonmark.org/0.30/#fenced-code-blocks

Styling is the way to go.

If you want/need to change the output structure rather than styling.
It is possible though plugins https://unifiedjs.com/learn/
Though is significantly more involved than adding a couple styles.