I had some issues doing any kind of free standing squat for a bit.
Sitting on a chair and getting up is a different physical exercise than doing a deep squat beyond 90 degrees unsupported. When you sit on a chair, you are not balancing on your feet only, with your muscles providing the balancing; you are fully supported.
The standing motion from a chair is vectorized into a forward motion which is supported initially by the chair itself, with the momentum supporting your upward motion. The legs push up, taking advantage of the forward motion to move your mass upwards with a smaller requirement of force. The hamstrings are rested and are not under stress. So the actual push upwards is lower due to the forward vector force, there is less upwards motion of the upper body needed, since the distance covered is less from a chair to a full standing position.
The standing motion from a squat starts lower, so the upper body has a longer distance to cover. The initial push up has little forward vector motion, so the bulk of the effort is in an upward push, with the movement lifting the entire upper body. The leg muscles in a squat are stretched supporting the overall weight of the upper body and the legs, while balancing the body. The initial push comes from unsupported leg muscles pushing the upper body up while balancing the upward rise.
Reverse the motions and you get similar stresses. IMO a squat is a much different animal than sitting and rising from a chair. I'd actually have fun figuring out the vector forces involved for both.
It is a good question, though, a reason given the stresses to avoid movements that put a lot more pressure on the body until we are ready for them. The more we understand, the better off we are.