Coming back from a knee injury I have decided for the first few months at least to pause squat, rather than perform regular weightlifting squats. By weightlifting squats I mean squats that develop the requisite qualities of weightlifting. The main ones being an upright torso and a deep bottom position. Of course I am maintaining these requirements with my pause squat, but the one characteristic I am leaving out is the stretch reflex.
There are some benefits to a pause squat. Perhaps most importantly they develop 'starting strength'. Starting strength is not just a book, it is the ability to move with a load out of a motionless position. Standing up off a box during a box squat requires starting strength. Pressing a bar off your shoulders without any hip or leg drive requires starting strength. It is a useful part of strength to develop, especially early on in your training career. But weightlifting doesn't really require any starting strength...
Starting strength comes purely from a muscular contraction - building tension and moving. A stretch reflex comes from the elasticity in the tendons, ligaments, and muscles. It is this that weightlifters use. We bounce out of cleans to try and use as little energy as possible to stand the weight. We dip and immediately drive in the jerk without a pause at the bottom of the dip. We even 'move before we move' in the pull: rocking on the heels to find tension and a stretch, or maybe a bob up and down to generate some movement of our own body before we act upon the bar.
So teaching ourselves the timing and movement of the perfect stretch reflex is a far more specific skill to weightlifting than the pause squat. I believe pause squats have their place far out from competition to develop a more general strength, but during the SPP (specific physical preparedness) of training I think that we must always bounce out of our squats. One thing I have noticed with the people I train alongside is that those who pause all of their squats have strong legs for sure, but they don't catch a convincing bounce in the clean. They either catch the bar with a dead stop, pause, and then stand up, or they almost absorb the weight or the bar before the bottom position with their legs and then slow it down before they are in the deepest position before actively reversing the movement of the bar as they stand up, instead of allowing their knees, hips, and ankles to time a perfect bounce. It almost looks like they are trying to protect their knees from the impact.
I have seen a correlation between lifters who get a tremendous stretch reflex in their squats and lifters who catch a nice bounce during their cleans.
So as soon as I feel confident on my knee again I will start bouncing out of my squats. I always have done so in my squats, and I always have done so out of my cleans.