There no such things like "universal best of all kamae". Sometimes your body/feet position must be aligned, sometimes must be square with parallel feet. All depends of the goal that you want to achieve. Paying too much attention to the external form may result that you will not develop any content.
As far as kicking somebody that has square kamae, this is very risky activity. We use to establish square kamae as an ‘easy target' as an ambush for those naïve minds who will commit to an attack. It is enough to turn hips in the moment of the contact to smash them down to unify with tatami, really no effort LOL
I have seen very, very few Aikidoka who if caught in a square kamae would ever be able to stop a front snap kick when the distance is close enough not to have to step to kick. I am not talking about naive minds, but experienced fighters.
Your general point about not getting too caught up in the external form is a good point that takes a lot of experience in kumite to achieve.