Think of functional movements as the movements you were born to do. Things like running, jumping, throwing, picking things up off the ground, lifting things overhead; sitting down and standing up are all functional movement patterns that humans have been doing since the beginning of time. These movements are your birthright!
All of the movements we perform in CrossFit are movements you should be able to do, if you can't why can't you? Let's go look at those 10 general physical skills and I would bet a million dollars your reason is on that list. So if we develop that skill to a greater degree you'll be able to do the movement. See, everyone walks in the door with a movement history, and injury history, and professional history (think about pattern overload in constantly varied) and all of these things effect the way you move.
Imagine a scenario where a person who hasn't done a deep squat in a decade or more has to get down that low. Now s/he's knee hurts so it's off to the doctor to get it checked. The details of the injury are relayed to the doctor who promptly declares that squatting is bad for and that's that. Here's the problem, it's wrong. In fact, if you consider that for most of the worlds population this position is a sitting/resting position. This is how people use the bathroom.
Part of the problem here is that people stopped looking at these things as movements and limited them to "exercises". Squatting is just sitting. If you are sitting on an object it may be high or low. We were born to move, not to exercise. We use squatting to explain the differing view on this subject but this really applies to any movement. There are biomechanically sound ways to move. There are ways to distribute your body to limit joint strain. You may need to regain movement that you've lost of the years, but do not be afraid of your body and what it can do. Embrace it!