Stinking cloud explicitly uses the words 'line-of-sight' preceded by 'blocks.'
Why would you not use the line-of-sight rules on an effect that explicitly mentions line-of-sight? Do you not use damage rules on effects that use damage, or saving throw rules with powers that use saving throws?
In my head, it doesn't make sense that an effect designed to -explicitly- block line-of-sight does not, in fact block line-of-sight.
Using cover and concealment rules make sense -if- you've established you can have line-of-sight. But -first- you have to ask the question 'Do I actually see this guy?' and if the answer is 'no' then the cover and concealment rules never need to come into play.
You first check the line-of-effect rules to determine if you have line-of-effect from the point of origin to the target. If you don't, then you might have trouble affecting the target at all.
You then use the line-of-sight rules to determine if you do, in fact, have line-of-sight. If these are failed, you cannot see the target, and the 'cannot see the target' rules apply.
Then you check to see if it has cover, if-and-only-if you have line-of-effect. Cover is a barrier interposed between the point of origin and the object. This is not the same as line-of-sight and has nothing to do with sight at all. Cover is an object that gets in the way of possible -lines-of-effect.- Cover is measured from the point of origin, not from the user of the power. For Melee and Ranged attacks, those are one and the same, but for Close and Area effects it might not be. The cover rules have buttkiss to do with seeing the target.
Then, you check for concealment, the other sight related thing. Total Concealment is simply 'you can't see the target'. Because you've already checked for line-of-sight you know you can't see the target, and thusly total concealment applies. Otherwise you'd check for obscured terrain/squares, which needn't apply in the case of stinking cloud, unlike with wall of fog which explicitly says otherwise. Concealment doesn't use lines-of-effect, candidacy or anything else. All it counts is if you can't be seen, and then the terrain you're in, depending on if he is adjacent.
The rules actually make sense if you apply them in the right order, and in the right situation.