We all know that row staggering (x-staggering) is unnatural and should be avoided. Some amount of column staggering (y-staggering) can be healthy because it takes care of differences in finger lengths, to some degree.
There is one more dimension of staggering, z-staggering, that I build all my boards with, so my fingers are at even more natural positions.. For example, [5,4,0,0,2,4] are the heights (in mm) of the six columns of the right split. With this, the boards are still quite compact and easily tentable. I think a keywell may not do much better than z-staggering.
A large thumb cluster can be too much burden to the thumb. The big one is not really that flexible and I've read others saying they only use two-ish of the thumb keys most of the time. (Caution, small sample size).