You are missing the point. The report doesn't compare miles driven with and without autopilot. It compares ALL miles driven in cars with Autopilot function, whether it is turned on or not, vs. cars without Autopilot function.
To boot, these are, for the most part, the same cars before and after, since Tesla shipped cars for almost a year with the Autopilot hardware built in but not activated, then activated it for all cars at virtually the same time via an OTA. Before that date, any miles clocked show up in the "no autopilot" column, the next day they show up in the "with Autopilot" column.
To further flog an expired equine, the study showed a 40% reduction in airbag actuations per million miles driven across all miles driven in cars with vs. without Autopilot function, not comparing only miles where Autopilot was turned on.
There are certainly possibilities for this data to be skewed or biased, but it's definitely not a comparison of safe Autopilot miles vs. unsafe manual miles.