In a nutshell, you have two targets that you can save per character: the focus variable, and the primary target. It does not matter if you click it, /assist or do whatever else to have the character select the target.

I currently do use /focus and [target=focustarget] for normal targetting and the regular target for CC, but only on the char that does the CC. Example, I want to sheep something. I select the to be sheeped mob as target on the mage's client. Since the mage never /assists or targets anything with focustarget, that mob will stay his target and default target for /cast polymorph whenever I hit the sheep button. Now, there is one drawback to this, and that is that when the main char is MCed, polymorphed or feared, target=focustarget does not work. In fact, sometimes I have to deselect the target on the main, reselect it, and only then my dps chars will fire again.

By doing it as the OP says, both the kill target AND the potential CC target can be saved on the dps characters, as their normal and their focus targets. That means CC on the main char does not interrupt DPS. Besides that, there is no difference to my knowledge.