I used to think there was no difference, until I picked up a job tutoring science students. I think test taking skills involve the "bandwidth" a person has for transferring information from their environment into their mind, processing it internally, and then transferring it back out to manipulate their environment. The person may have a great fast "processor", but the bitrate of uploading or downloading information in and out of the brain could be very low. Dyslexia is the classic example; I tutor a couple of very smart students whose test scores are low simply because they don't read and write fast enough. They have to work for hours to absorb concepts that another person could grasp in 10 minutes, but once they understand, they demonstrate just as much facility applying the knowledge.
The MCAT requires you to read and think FAST, more than just about any exam you're likely to encounter in college. You have to jam all that data into your mind and come up with the correct answers quickly. High-bandwidth/fast processor people are rare; it is a gift for which the MCAT is intentionally selective. It gives "normal" people a taste of what a learning disability feels like. I think that may explain why someone could have a high GPA and a low MCAT score.