Which specific app versions and operating systems are causing issues? I will include them in the list for analysis.
Did you use StillColor or BetterDisplay to disable dithering?
What monitor are you using (8-bit, 6-bit+FRC, etc)?
What Mac do you have?
On macOS Catalina, which has no significant dithering in the OS (I know of)
However the newer Chromes (>= 120) and Transmission 4.0 on it really annoy me, very hard to look at. Chrome specifically has this weird "sleek" look where everything is very sharp and blacks are very black.
But it's fine I just use older versions of them
On macOS Catalina
Sorry, I can't perform the analysis on macOS Catalina because I have only an Apple Silicon Mac.
On Apple Silicon running Sonoma 14.1.2 and Chrome 133, any flickering is absent (I use StillColor). Perhaps the browser's rendering engine has color settings that make the rendering result more contrasting. I have noticed that a high-contrast and sharp image strains my eyes, and perhaps the same is true in this case
Yeah it's fine I just use older versions.
But basically, it seems even single windows are able to introduce temporal dithering on macOS (even when otherwise there is none) 
Adding this here because I'm positive a Mac OS version difference causes it on identical hardware. I'm still leaning toward "temporal dithering" being the cause and I'm locked at Mojave on a 2013 MBP. Updating to Catalina caused in instantly so I reverted. When that laptop died because the keyboard could no longer be repaired I bought the same hardware model which had been updated to a newer OS and caused strain issues. I used a factory reset and time machine backup to boot into Mojave and it was fine again. On this machine for my eyes Catalina OS and newer were the culprit.
Recently I accidentally updated Brave browser and somehow even on this OS/Hardware the browser itself seems to have introduced dithering (newer Chromium?). Others have reported it being related to the hardware acceleration setting but there might be a bug preventing it from stoping when I turn it off. Firefox is fine so I've switched over.
It's a software/driver issue or a complex web, not simple hardware. Friends have suggested simply using an older monitor but you can plug in a 1920x1080 monitor from 2010 into a new mac and it will be nauseating. It's a software/driver thing. I'm positive of that.
Similarly, Windows/Linux seem to be copying Mac- or is it the GPU companies? Unsure but I'll get the same effect on an increasing number of non Mac computers.
I hope to try higher end monitors like BenQ and one of the nano-coated screens from Apple, as I've heard some have success with them.
This seems like proof that applications can introduce dithering so long as they’re running? Was this limited to the browser window itself?
Absolutely wild that this is even a possibility, especially on systems that are allegedly disabling dithering on a system level (Stillcolor, SwitchResX, Betterdisplay).
AshX Not to muddy the waters, I just want to mention that this Brave browser thing on the old computer causes maybe 10% of the issues compared to anything on my Silicon iMac, which is instant nausea even with Stillcolor. No idea what's up if that's actually working. I could deal with Brave Mojave if I had to.
issues compared to anything on my Silicon iMac
The issue here might lie in the display itself, rather than macOS or the GPU. The display of your iMac is wide gamut. Such displays often use technologies that can strain the eyes significantly on their own, even in the absence of PWM and dithering. Moreover, Apple does not disclose the exact specifications of their displays, and it’s possible that some colors are rendered by the display using temporal dithering (FRC).
WhisperingWind Just to mention though, on this old computer from 2013, when I update to Catalina it feels nearly 1:1 to the modern iMac despite very different display hardware. This indicates to me that it's more of a "how the hardware is being controlled" rather than "what are the physical limitations of the hardware" problem. Maybe the terminology hardware/software/driver can add their own difficulties.
WhisperingWind The color Gamut issue is interesting though and I'd like to understand more about how it works. I've done tests like creating interfaces or web pages with only two colors. It's my understanding that we still get the nauseating effects because on the edges of rendered text there's dithering applied to smooth black to white or one color to another. In some sense there's not actually a way to control individual pixel colors- everything is smoothed in transitions and flickers to have more color gradient that what is possible on the display.
The color Gamut issue is interesting though and I'd like to understand more about how it works.
When using KSF phosphor (which can be applied to LED backlights in wide gamut displays), there is a slightly reddish tint mixed into all colors. This is because KSF phosphor emits light in the red region of the spectrum, which enhances the saturation of red colors. However, this can also lead to changes in the spectral distribution of emitted light, affecting the overall perception of colors. Some people may be more sensitive to changes in the light spectrum, especially if there is a strong peak in the red region. For me, this creates a sensation of a "reddish tint" and discomfort during prolonged use of such displays.
amusesmile I’ve had a similar experience, with browsers specifically. I have a 2017 MacBook Pro 13 without Touch Bar. If I use it on Catalina with the built in Safari version 13 it’s fine. If I update Safari past that I get eye strain but in Safari only. I noticed this phenomenon starting to occur in other browsers around the same time MacOS Big Sur came out. First Safari (versions 14+), then Chrome (unclear which versions), then Firefox after 122/ESR 115.7. The current versions pretty much all cause eye strain now for me on MacOS despite the underlying OS UI and other included apps still being ok with minor settings tweaks. I think it corresponds with the increased adoption of newer web standards for color management/hdr/wide color starting around 2020/2021 but I don’t know for sure.
I currently have Mac OS Ventura installed on it and I don’t have an up to date browser that is 100% ok eye strain wise. But other stuff besides the browser is more or less ok.
amusesmile Updating to Catalina caused in instantly so I reverted. When that laptop died because the keyboard could no longer be repaired I bought the same hardware model which had been updated to a newer OS and caused strain issues. I used a factory reset and time machine backup to boot into Mojave and it was fine again. On this machine for my eyes Catalina OS and newer were the culprit.
This mirrors my own experiences. I have a Mojave Macbook Pro 2103 in front of me.