While it might be guessing, there is some science behind it. At these extreme times, either WR or near WR, there just isn't enough data to refine it.
KB ran 28:59 (4:40 pace) to start Berlin, and then ran 3.25 more 10000s in the 29s. That surely means the 28:59 was exceptionally easy.
Also, when Geb ran 2:03:59...he was coming off a 27:06 10000 in Beijing, a hot championship race (at something like 37 years of age.)
We know Bekele is better than Geb. Bekele is younger than Geb, and now almost a minute faster over the marathon.
I infer from this that Bekele at worst in 26:50 shape.