It bothers me because I have an iphone 4s with the latest possible os that works on it (9. something) and no issues whatsoever, and when I put it next to the iphone SE, just browsing my eyes between them I feel immediate difference. But the 4s is also retina screen, the OS is also fairly new. It is just confusing.
I feel like then it must be something physical, not OS related. But SE has no PWM reported. Regarding dithering, who knows, newer display, millions of colors and all that bullshit might be the reason. The display IS yellow tinted compared to the 4s though. I guess it might be dithering that makes the SE unusable but cant tell.