It is the keyword CTR that matters and NOT the AdGroup CTR (or the ad copy CTR or the campaign CTR) when it comes to deciding the ad position.
Because it would be unfair to use, say AdGroup CTR, because you may have only 2 keywords in an AdGroup while your competitor may have 5 keywords. If your competitor having 5 keywords manages to get hold of a high-traffic/low competition keyword and inserts them into the adgroup, his/her adgroup CTR may shoot up.
AdWords system will not "penalize" you for not discovering this high-traffic/low competition keyword. The ranking of your ad is always "comparative" - hence it takes the keyword CTR.
AdGroup CTR/Ad Copy CTR/Campaign CTR numbers are mentioned so that you get an overall picture of your campaign performance.