I agree that these cases are ridiculous to blame on the waymo entirely, but to give logic to their reasoning here you're unsure if on average the 1.3 fatalities per 100 million miles (FPMM) may also be on average ridiculously not the drivers fault as well. Perhaps if you were to throw out all ridiculous cases you'd have an average of CDL's having a 0.3 FPMM vs Waymo's having 0 FPMM.
The nuance you describe at the end is the better interpretation: fatalities per mile driven is a useless metric since it's such a rare occurance and incredibly circumstantial that it cannot be used as a meaningful comparison metric for safety.