i guess I can see the arguement for kipping, but in no way does it make them more difficult, it clearly makes them easier, so you may accomplish more of them (you said so yourself). It's cheating to accomplish more reps if you compare them directly to pullups
crossfit is no joke dont get me wrong,there is a reason that many SF guys use this, but i think you should have made your focus to build your cardio and not primarily strength. Maybe you did but people can't get past the kipping thing because it's not commonplace in a gym.
Your chest to bar arguement is not very good , use the same standards on your pullups and you will probably burn out even faster. The reason you get your chest to the bar is becasue of momentum, not because your form is better or your using more strength. It's like the guy in the gym that curls 60lb DB's but swings the weights and lean's back.
Crossfit is a great variation for many guys looking to get into shape, but not for weightlifting and bodybuilding. For the ordinary joe, I don't know where you'll use this so called functional strength, because you gain fuctional strength from just weight lifting. If you want to be technical weight training, and Crossfit both are not used everyday for a vast majority of the people who train their way. We do the exercises because we enjoy it, and it makes us look the way we want to! Everyone has different goals for their body, and this is a great cardiovascular progarm with strength training. If you haven't tried it, try and and you will be hurting no doubt.