The 9.2.0 ctrtransfer image brings in default "flicker" values set for the top and bottom screens. They apply only if you format after doing the ctrtransfer, however long later that may be.
These are numbers from 00 to FF that Nintendo calibrates before shipping a 3DS. If they're approximately right, you won't notice any difference at all. But if they're off by maybe 0x20 or more the screen will appear brighter, somewhat washed out, and flickers in a 1x1 pixel checkerboard pattern when there's motion. The further off it is, the worse it looks.
I did the 9.2.0 ctrtransfer after restoring the NAND backup I did with D9 after the 9.2.0 downgrade, because I was getting repeated errors from system update. I then formatted for no particular reason at all, and found my top screen suddenly looked brighter and odd.
The only ways I know of to fix it are to restore a NAND dump or configsave from before it was messed up, or using Nintendo's config menu app to recalibrate it like they do at the factory. I found the config menu app on 'that iso site' by searching for "Retail Encrypted DevApps" and downloading the one containing Config_v11_4_NAND.cia. You select LCD config, and select which screen. It shows a gradient on that screen and you adjust the value up and down until you find the value that makes the left side of the gradient darkest, and the whole thing not flicker.
I don't know if the ctrtransfer image can be modified so it doesn't pull in potentially bad flicker values that will be applied on the next format, or if users need to be instructed to use the config menu to fix it if they experience odd looking screen(s).