That article makes sense - the dealership can't actually tell what/if the programming has been changed but can see the flash count.
I know in the case of subaru with warranty issues(at least on wrx, sti) subaru canada also requires pictures of downpipe/exhaust to look for new/altered bolts and nuts that signify changed/replaced parts.
The only way to actually check the programming of an ecu is to send it back to the manufacturer. The dealers can only identify the flash count.
I have heard/read that some tuners have a way to reset the flash count while tuning.