Pass-through as far as I understand means the HDMI signal stays in its original form, unmodified, including any dithering.
I think temporal dithering, which comes in many forms, could be smoothed out at least a little via scaling or other image manipulation that takes place after the signal has left the input device. If we had full control over a man-in-the-middle device, perhaps we could implement our own scaling algorithm. I don't know if this can be done without owning a company and if the required hardware would be cheap enough. It may be worth to investigate further.
However, regarding the Raspberry Pi: I think it's true it doesn't have temporal dithering enabled by default - yet it's not usable for me. I believe there are other reasons beside temporal dithering especially for this "Linux eye strain" that not only affects the Raspberry but also PCs in general. Whatever it is, it causes eye strain even when no desktop element is being moved. It is really difficult to pin it down.