In version `5.5.0`, `github-markdown.css` uses `--base-size-8` and `--base-size-16` vars for `.markdown-alert` and some other elements. However, these are not declared so they defaut to `0`, removing the padding from alerts. `github-markdown-light.css` and `github-markdown-dark.css` don't use this vars, they use `8px` and `16px` instead, and alerts render properly.