As a dark mode user, I'd also like to add that I find this very distracting when reading equations in a PDF: both the fact that any superscripted number appears to be perpetually highlighted, and the popups that come up when I'm moving my cursor over the equation as I often do when reading. This happens to me particularly frequently since most of the papers I read using the Zotero reader include equations. I would love if the team added an option to disable this, or options to reconfigure it as part of a style template or something, (maybe even with user-defined regex).
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