Allow me to weave a bit of bullcrap.
I have never seen Knott play so, stats aside, my knowledge of him is all imagination, where he is an amazing keeper and a solid batsman. Based on prevailing views, it seems clear that Knott was the better keeper and Gilchrist was the better batsman. How much better does Knott have to be to edge out Gilchrist? There would be a balance somewhere, where the chance that Gilchrist fluffs and loses a game equals the chance that he plays one of those innings that wins the game. In my mind, Gilchrist is at about that parity.
In an all time team, full of great bowlers, he can only play against the second all time team, full of less great batsmen. So this attack would be creating more chances than normal. Therefore, I think Gilchrist would fall on the side of his batting winning more games than his missed chances lose them, as the better bowling lessens this effect. In Knott's case, being in the All Time 11 and playing against a second 11, his batting would be solid, but not match winning, while the amount of chances created by bowlers would dilute the reward for his great keeping skills. I think his net effect is less in the all time great team. He is better placed being in the second 11, where his solid batting would be more effective against the all time 11 bowlers, and his better keeping would help make sure his lesser bowlers had their chances of missed wickets minimised.
For this particular moment, I guess I am thinking that with better bowlers than batsmen, take Gilchrist. With a team of better batsmen than bowlers, take Knott. If you can't decide which role is better, then who cares?