This dark mode topic came up in the past, and I commented similarly. One (typically knowledgeable) HN reader replied to my comment with an explanation about this. I would have to really dig to find it though...
I'm not sure, but I suspect that in general, dark mode syntax highlighted (highlit?) text is on average lower contrast than syntax highlighted light mode text. That could affect compression behaviors, perhaps.
Kind of off topic, but I've always wondered why this is an issue. If I invert the colors, will those parts of the image suddenly compress just fine? Is it something to do with human perception of dark colors (like how many compression algorithms use more detail in various characteristics we're more sensitive to, such as brightness, as opposed to color)? That wouldn't make sense to me, as it seems to be a pretty obvious visual flaw.