Yes, it's calculated across the population, it's an epidemiological study. That is, for every million hours the population as a whole spent driving, there where 0.46 head injuries (as an average). For every million hours the population as a whole spent cycling, there were 0.41 head injuries. This was before the helmet law went in to place. This means that, on a time sent basis, you where slightly more likely to receive a head injury in an automobile than on a bike. Your math would be correct, but the probabilities you listed are not those the study found.
Meanwhile, this study found that whole helmet use in Victoria and NSW increased from roughly 30% to roughly 75%, the proportion of head injuries only dropped by 13%. On the other hand, ridership declined after the helmet laws.
Raising more questions, during the same time period, the proportion of head injuries amongst pedestrians also declined by about the same amount, indicating that helmets may have partial or no responsibility for the decline.
Again, the available data suggests that without helmets, the rate of head injury stays in line with cars and walking, and with helmets, the rate stays in line with cars and walking.