Quoted from RavagedUnicorn:
That would still work. Pinheck would also read the chucksum from a specific location. If you write the data or checksum anywhere else, it'll fail the check.
By using a common format (FAT32 in this case), they are making it very simple for anyone to copy the data to the SD card. However, in that scenario any checksum would be read on that higher level format whereas the actual memory locations would be determined by the low level format (using hard drive terminology as I'm from a decade behind this technology). So a checksum comparison would be handled on the PC through FAT32 unless a program was written to analyze the low level format, which is orders of magnitude more complex. The alternative would be to use an image of the ROM and then have some sort of bootstrap that writes it to the EPROM, but I have a feeling that would introduce its own set of problems - and I'll flat out guess having Pinheck do the hard math just isn't an option. It would need not only the processing power but also the RAM to do the work in; I'll bet a case of beer that Parker isn't trying to hear that.