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There are two problems here: one that the color is incorrect, and another that the background color is applied just to the text and not to the whole square.
For the first problem, I need more information for reproducing it. On my Emacs I don't get the gray background at all, and if I try customizing e.g. markdown-pre-face, my customization seems respected by htmlize.
For the second problem, I don't know if it's possible to get that effect in the browser (inside a <pre>). If someone can show the desired HTML output, I'll make htmlize emit it.
Code blocks for Markdown file are rendered "incorrectly" :
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