Kind of. It's useful to see the per distance and per population figures. You are likely to drive more when you are in the USA compared to Europe (due to the culture and bigger distances to travel) and this increases your risk.
If I was analyzing my total risk of dying in a road accident, both figures would play a part.
As someone else mentions, I think that drivers pick lanes at will leads to constant lane changes and also to traffic jams and reduces throughput. That to me is a huge thing that needs fixing. It also makes driving much more pleasant. You never have a "wall" of three slow cars in front of you and now have to figure out which one of them will eventually make way, so that you can pass and now everyone has to change lanes. It's insane! In addition to the broken "protocol" that's being used on roads cars are also much less save. Lots of pickups have these pipes on front of their car's grills (sorry no idea how those things are properly called). These are actually illegal in Germany because they increase injury likelihood for pedestrians. Trucks in Europe have to have barriers on the side, so that in a collision they push a car aside and have a big impact area, rather than just hitting with a car with the edge of the trailer just at the same height as where people's heads are. Really cheap to do and would save lots of lifes. There are also many more very large cars in the US. If those crash into a smaller car that can have much more severe consequences. I think the lack of monster pick up trucks in Europe helps. I know many people here get these trucks to defend themselves against other people who are in these huge vehicles.
The deaths per vehicle-kilometer figure doesn't illustrate that it's very difficult to opt out of the automotive dangers in the US. And thus we also have a hard time forcing dangerous drivers to stop driving, in order to keep the rest of us safe from them.
Intuitively, if two cars each average one death per million miles, but one of them had an average speed of 5mph, and the other 60mph, then the faster one should be regarded as safer because it maintained that death rate under less safe conditions.
1. Deaths per 100,000 seem to be pretty good a measure for pedestrian deaths
2. Your measure does not consider the cost of driving more
But, one point I think you have: If indeed the number of deaths per km is similar, then the solution to car deaths is to drive less, not to drive more safely
According to this[1] list of traffic-related deaths by country that includes deaths per billion vehicle-kilometers (also not a great figure, but better), the US has 7.6 and Japan has 8.3---Japan is more dangerous, not much less. Spain is the same as the US, France is 6.3, and Germany is 4.9.
According to the IIHS[2], Montana as 1.96 deaths per 100 million vehicle miles, while New Jersey has 0.74, a factor of 2.6 vs 3.7 according to the article's deaths per 100,000 people.
[1] https://en.wikipedia.org/wiki/List_of_countries_by_traffic-r... (WHO data, 2013?)
[2] http://www.iihs.org/iihs/topics/t/general-statistics/fatalit... (2013 data)