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MathJax only processes TeX that is within math delimiters. In your case, those are the \begin{equation} and \end{equation}, so the % etc is outside of the mathematics, and MathJax does not handle that. It is part of the rest of the HTML document, so follows HTML rules, not TeX rules.
Issue Summary
Using your demo with this piece of code:
Is rendered like this:
You see the "lost"
% etc
after the equation?Technical details:
Your demo with current Firefox from latest Debian 11.
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