Assuming GCD is 1 sec and fights last longer than 3 seconds -
Why ever use Kill Command?
I do 1100 Damage with Arcane Shot for 20 focus, and I do 1300 damage with Kill Command for 40 Focus.
If say you only get to use 3 spells in a fight, then yes, kill command is going to do more damage. 3 Kill Command drains full bar of focus and does 3900 Damage.
Now if a fight lasts longer than 3 secs:
4 Secs with arc shot = 4400 Damage
And it only scales up from there. So why would I ever use Kill Command?
You're asking what it's use is out of context as the burning man effigy of a sec fight being exagerated kinda is overplayed. Also asking about 'Why would you ever... ?' about anything without first actually looking at max level scaling shows you to be ignorant of anything truly relevant to your question.
That said in general Arcane shot is much better damage per focus at most levels BUT short of mobility fights pre steady/cobra on move it will never result in better damage per second. Why is that?
Cobra shot = 70% weapon damage + 6 seconds to SS +14 focus
Arcane shot = 100% damage + 2302 at max level(this is easily only 20% damage at most once decently geared max level) + costs 20 focus, (for easy math calling this 120% which is generaous in favor of your argument)
Kill Command = RAP scaling ability but will be asumed to be 200% damage as this is lowballing it to defer to you argument making it more likely it's not needed the higher it is the more you would want it + costs 40 focus (scales directly with additional mastery and pet frenzy as well)
For napkin math we will assume ALL passive focus regen is being used on arcan shots and is being discounted as being equal. Also assumes no haste or crit as they scale linearly in relevance to this argument. Mastery is being assumed to be 0 but more mastery favors Kill Command use.
So now to be focus neutral you will need: (Focus neutrality is only consideration for being in relation to eachother as all others will be consistent and equal exclusive of these, ie auto shot damage, passive focus regen used on arcane shots etc.)
NO Kill Command for ~30 sec of the rotation
10 CS + 7 AS = 700% + 840% = 1540% damage in 30.5 seconds (50.5% weapon damage per second change to dps secluded from mastery, haste, crit all which are equal or favor KC directly)
WITH Kill Command for ~50 sec of the rotation
7 KC + 20 CS = 1400% + 1400% = 2800% in 50.5 secs (55.45% weapon damage per second change to dps secluded from mastery, haste, crit etc)
End result direct relation there is a 10% portion share damage increase over not using KC BUT in your total damage rotation including all other factors (arcanes from passive regen, Auto shots, crit, haste) KC roughly would be safe to assume about 2-3% edge at most but KC is more and more desirable the more mastery you have AND is mandatory during BW use as pet damage is increased 20% your's is only increased by 10%