It is possible that the percentages aren't accurate. For one, when talking about long distance runners, it is hard to get an accurate gauge on how fast they can run the 400 meters. 49 vs. 53 might not represent what Geb and Meb are actually capable of.
Regarding their 1,500 times, Geb ran 3:31 at the World indoor championships. When has Meb run a 1,500 meter race at a major championships? As far as I know, he hasn't, therefore his top 1,500 meter speed isn't known. Heck, not even milers who run the 1,500 meters on a regular basis run close to their personal best time every time they race. Not unless like Hicham El Gherouj, they have a rabbit.
Geb and Meb's 5k-10k times do compare favourably. Therefore, I conclude that their VO2 maxes also do so.
I think the difference lies in their basic leg speed. Because Meb is slower, he has to use more muscle fibers in order to reach a speed comparable to what Geb can run. Therefore, he would have to use more energy.