Well, you need to go back to his original publications and to his first book (I think it was his first) called Oxygen Power to see the actual calculations.
You're partly right to assume that your running efficiency might be lower than the perfect runner. However, there are those out there whose VO2max measures lower than the VDOT that their race times would indicate. Does that mean they are 106% efficient? No.
A LOT goes into how those tables are devised. Keep in mind that VO2max and your vVO2max (velocity at VO2max) are important in short races, and maybe up to 5k if you're decently fast, but in longer races, other factors become more important - like the percentage of VO2max pace at which you start to accumulate large amounts of lactate. In other words, is your lactate threshold at 80% or 92% of vVO2max for example. For me, I had my actual VO2 max measured at a 74 twice after I was out of college and was 'fun running.' I was not racing at that level though. I was racing anywhere from 66ish in short races (1500, mile) down to 58ish in 10k and longer. For one thing, I was not putting in much mileage. For another, that same VO2max test showed my ventilatory threshold (which occurs at a similar point as a lactate threshold) to be about 80% of VO2max. So, not very high. This explains why my VDOT scores dropped off fairly sharply the longer distances I ran.
Do not equate VDOT to VO2max. It is NOT VO2max. Also keep in mind VO2max is actually a fairly poor indicator of race times among fit people. Many many factors go into racing, from lactate, to cardiac output, to psychological abilities to push one's self, to stride mechanics, to carbohydrate storage and fat utilization, etc, etc, etc, etc. You get the point.
Use VDOT for a framework for training and it can truly help you attain goals. But it is not meant to be VO2max.