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.