The reason you had to read it in bootmode, and the errors are related. I'd be willing to bet you have an APR (or other mainstream) file on your hands. Open it with a hex editor and look for ASCII (Text) strings.
As for clearing the checksum DTC, it can be done by manually editing the eeprom (95040) contents. Take a look at the immobilizer sticky, and scroll down to the "death code".
The file is definitely stock. I do have an additional ECU with APR software (that's in the car now), but it had the rear O2 sensors deleted by APR, then I removed the SAI system, so it won't pass inspection, hence why I'm playing around with my stock ECU. I have seen the ASCII strings in GIAC files before, and nothing like that in this one.
So, just to be clear, you WILL cause checksum errors in the read file when reading in boot mode? If I never wrote anything to the ECU, would the ECU itself now have checksum issues?
Thank you for pointing me to the "death code" immobilizer section, I will look into that.
Extra Info - I had tried using ArgDub's tool to read the EEPROM previously, but wound up getting an error at the portion where it was loading monitor services (or something like that). This was at the slightly higher voltage which had failed with Galletto. I never tried again after a successful Galletto boot mode read. I also didn't play around with lower baud rate settings. I will try tonight to read the EEPROM and store a working copy (hopefully it doesn't already have an error). If I have both the EEPROM read and the stock flash bin, would writing these both back to a bricked ECU (assuming they are error free) fix any potential future death code issues (I just want to make sure I have a proven tested way to restore from the worst case scenario before going further)? Also, would the death code show up if I ran VCDS on the bench, conversely, if it doesn't show up, but ME7Check shows 3 errors, is there a difference between my bin on my pc and the bin on the ECU? Does this mean bootmode does not read a true exact copy?
Sorry for my newbishness. I really appreciate everybody's help here, between helping me directly and just documenting these things to allow people like me to learn through the archives and trials of others.
I started reading about the Death Code issue (thanks for the thorough writeup ddilenger!) but need to dedicate more time to really absorb the material.
p.s., here is the file in case you would like to take a look.