I have been comparing BIN file and DUMP file from EC, even when I compare my faulty flashed 8100Y EC dump with 8100Y bin I see differences, not something like padding I guess. There is a kind of pattern in it. Maybe flashing from the USB stick operates on a different way and does alter the flashed content while writing (security or something?). Our best option would be a full BIOS dump and full EC dump from a working system. That way they are perfectly matched if any checksums would be active.
Did you check that you are at the correct voltage when reading/writing the EC memory chip? The BIOS chip and EC chip both operate on a different voltage, which can result in unreliable readings if you use the wrong voltage with your programmer.
When I have some spare time I will pick up this project again.