Yes, it seems the "why" here is more interesting than the "how", and is indeed going to be a matter of speculation.

As far as evolution in general, the big picture is more about "punctuated equilibrium" than incremental change. Individual genetic changes from parents to child are typically just benign and so accumulate in any inter-breeding population without much effect. Once in a while the environment may shift in some fairly major way (easier for environment to change quickly than genetics) and then an accumulation of previously benign changes may suddenly become collectively impactful in a positive or negative way.

I don't see any reason to assume that square poop was ever selected for - maybe it's just a harmless consequence of some genetic change that was impactful in another way. Speculating that square Wombat poop evolved to not fall off rocks is a "just so story" that raises more questions than it answers.