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ISN, VIN, and some other data is excluded from checksum calculation.
Look at the winkfp hex flash files. All get the same checksums when flashing, not dependent on ISN (which WinKFP never touches).
I correct checksums all the time as needed, and ISN modification never requires it. And you would easily get DTC for internal error.
But your point about different flash chip revisions is curious, because I have had some MS43 that accepted new ISN. MS45, never. Just my observations. I have easily done over 50 DMEs on desk.