It looks to me like all of the CM flights are on the old-style 737-8's, so the AV business class should be nicer and the lounge is better. There is one CM routing that goes through BOG, and that is on 737-7's, which is something I avoid if I have a choice.

That said, I would prefer to transit in PTY than BOG. In particular, because BOG, due to fog and airport congestion, is much more prone to delays. I would risk a short connection in PTY, but never in BOG, especially if the risk meant an overnight stay if I missed.