Why do 可不 and 可不是 by themselves imply agreement?
可不，可不是，可不是吗，可不就是吗，etc are colloquial phrases to agree what the other has just said. 

I'm not quite sure of the exact underlying reason, but I echo your suspicion -  perhaps it's a rhetorical question like "Is it not?".

However, we should be cautious that sometimes it can mean negation too as in the OP's example: 这可不那么简单. In this case, we read as 这可/不那么简单. If you add 就 and 吗 in the sentence: 这可不就那么简单吗，it becomes a rhetorical question, meaning Isn't it that simple=it is that simple. 

So, the way to determine (negative or positive) is based on the syntax and context. If 不 goes with 可，then it's positive. If 不 goes with the other part, then it's negative.