In the UK BA policy is that their website will always offer the cheapest fare irrespective of class on one of their flights. They seem to acheive it and it's probably about the way they don't pay commission to agencies who then have to add their own fees. I've no doubt some agencies match the BA website for price and occasionally you can get a better price from an agency but that's the policy so if Kayak don't consider airline websites you could be missing a trick if you want to travel on BA and you're based in the UK.