Your question is an interesting one, and I remember thinking about it at the time I became aware of the color difference. What colors I see are highly subjective – colorblind people don’t know what they’re missing until someone points it out to them (as in, “wait, you’re saying my shirt is PINK??”).
Like most colorblind people, my deficit is red-green, but “blindness” isn’t really an accurate term, it’s better to think of it as a deficit in color differentiation. I can see any color (as far as I am aware), if it is big enough. I can differentiate between the WK colors on my big computer screen if I pay attention to them; it would be more difficult if I used my phone, but I don’t do that anyway.
I believe what happened, in my case, is that because I don’t trust in my ability to see colors, over time my brain assigns less weight to their importance. It simply hadn’t occurred to me that the background color meant anything until I happened to read it in a forum discussion. So, in answer to your question, I’m not sure if customizing the colors would make that much difference. Hope that makes sense.