Why do 可不 and 可不是 by themselves imply agreement? It seems a little strange that


  可不 and
  可不是


(by themselves) imply agreement (something like 就是).  The textbook 标准教程HSK4上 has some examples, e.g.: 


  A: 没想到咱们毕业都已经十年了。
  B: 可不是！时间过得太快了，真想大家。


I'm expecting there's an underlying reason for this I'm unaware of.  Perhaps it's a rhetorical question  like "Is it not?"

Question: Why do 可不 and 可不是 by themselves imply agreement?

It seems like they should both mean "but no" (i.e., disagreement).  Indeed, they also mean this, e.g. (sourced from YouDao):


  然而，这可不那么简单。
  This will not be easy, however.
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.