VS Code's syntax highlighting is written with the TextMate grammar. It's a grammar that makes heavy use of regular expressions. So make sure you brush up your skill on backward/forward references and lookarounds, because all these can be used. TextMate is a greedy grammar, which means that unlike normal regular expressions it will not backtrack. Once a match is found, that will be used. The other important thing is that the grammar can be nested, but children of a match can exceed the parent match and therefore push the boundaries of the parent match.
A good document to read in more detail about TextMate: https://www.apeth.com/nonblog/stories/textmatebundle.html
The grammar for pug and markdown is written in JSON. You can edit that directly. The main grammar is written in yaml because that's easier to structure than JSON. However, VS Code expects a JSON format. Therefore you need to run the build:grammar script afterwards. This will produce a JSON version of the file. Afterwards you need to restart your extension window for the changes to take effect.