RE: Box squats
The box squat can be useful in building the standard squat because it forces you to kind of stop at the bottom before pushing up. This is harder, so your standard squat can go up.
Many of the guys do them at my gym, but as I think you're pointing out, if you plop down on the box, you can compress your spine with the weight. I recommend two safer alternatives.
1. Use a cardboard box or square piece of foam. This allows you know where to stop and begin pushing upwards but also gives a little in case you plop down too much. Obviously, you do these inside a power rack with safety pins.
2. My experience is that bottom position squats done in a power rack are harder but more productive and safer than box squats. I try to encourage guys to do these instead, but any exercise starting from the bottom is harder, so not everyone listens.