That's how variability is defined, yes, on groups (or, technically, on "probability measures")—which might be the entire population or a subgroup thereof. The term "subpopulation" isn't defined, and it isn't explicitly stated whether the high variability is a heritable trait. I believe your contention is that that the overall population has basically the same genes, everyone rolls the dice, and then the subpopulations are defined post hoc in terms of the resulting quartiles (or x-iles). Mine is that the subpopulations are genetically distinct and their die rolls behave differently.

Given that the paper is about evolutionary mechanisms and whether one group "prevails" over another, I think my assumption is reasonable; and I think that, given my assumption, the paper makes good sense in the examples under discussion.