Ultimately it's the format. It's less to do with the black background/white text combo and more to do with larger text blocks and less visual movement than traditional VNs (using your example, the background that's an actual scene: in full VNs those change, which create a kind of visual movement that alleviates the whole burning text in your eyes, in addition to there usually being less text per screen with larger text blocks interspersed only occasionally). It's the same reason a lot of people can't do ebooks that don't mimic paper and ink: it's just good old fashioned eye strain.
I don't think changing the background would do much but burn a different image into your eyes 😅 it's probably got something to do with the glasses in the sense that it affects you more strongly, but I think the best thing to do is what you're already doing and take breaks. It's a lot of words so it's kind of surprising no one's brought it up before.
I'm glad you like it though !!! Even with the visual attack 😅😂 💕💕💕💕💕