I would be curious to know what the numbers look like if you broke the driving up by city/highway or something like that. I'm guessing the deaths per passenger-mile are very different between the two.
They're also somewhat difficult to compare at a nationwide level because driving in the suburbs is not really comparable to biking in the city, in part because the miles per trip in suburban and rural areas are so great that biking and walking aren't really feasible, anyway. This poses a big selection bias problem: What if the real underlying effect is that suburban transportation is generally safer per mile, perhaps even independently (as much as they can be separated) of transportation mode? For that matter, are we even measuring the right thing? What if the metric that really matters is deaths per passenger-hour, or deaths per passenger-thing-you-need-to-get-done?
City driving and city biking or city walking, on the other hand, can be much more comparable. For example, I own a car, but typically use a bike to buy groceries. In part because, where I live, it's the quicker and easier option. Similar story for driving vs. walking to go to my favorite restaurant, or to go to the hardware store.
Finally, I think we'd be remiss not to think about how it's being framed: The original data focus on likelihood of being the victim of an accident. It's maybe more properly called "deaths experienced per passenger mile." The numbers would look entirely different if they were framed as "deaths caused per passenger-mile." That's kind of a big deal, because one framing suggests, on an instinctual level, that cars generally increase public safety, while the other, I'm guessing, would suggest that cars generally reduce public safety. It's the difference between saying that Elaine Herzberg died because she was walking across the street, and saying that she died because an Uber self-driving car hit her.