In general, the box squat has a better carryover to geared squatting than raw squatting. A geared squat uses less bounce out of the hole. It can be done with a wider stance and allows you to sit back much further. These things can be emphasized while box squatting.
For a raw squat, the box squat isn't as effective. This is mainly because the raw squat needs a rapid bounce out of the hole and a push off the hamstrings at the bottom. By using a box, this alters your technique and style. You're learning a different way of squatting. I've seen many people use the box squat for raw training and consistently fail at the bottom without the box. The strength, timing, and tightness are all alien when the box is taken away.
Obviously, free squatting while using gear has been used for years and has been proven to work. The good thing about using a box is that you aren't as sore after training, so your recovery is certainly better. However, the fact that you aren‘t as sore should tell you something—you aren't using the same muscles as you would during a free squat.
Another popular argument in using a box for squatting is that it allows a lifter to know where parallel is. For a raw squatter, this is a ridiculous statement. At some time, you're going to have to learn where parallel is and it might as well be now. Get rid of the damn box, grow some balls, and get down there. Even a light tap on the box (which many people use) isn't a good idea. You're still searching for the box and altering your form. You can‘t learn how to effectively bounce out of the hole with a box underneath you. Well, I guess you can, but that‘s your spine, not mine. So stop pussyfooting around and do it right. With gear squatting, a box should be low enough to illicit results and offer proper form while being high enough to save your hips. Because most people who wear gear use a stance wider than shoulder width, the squatting can take a toll on your hips. I highly recommend using briefs or a squat suit (straps down) for your sets.
If you use a narrow stance and wear equipment, the choice is yours. However, I recommend using free squatting rather than box squatting in your training. This is because a narrower stance, even if you use equipment, uses a bigger bounce out of the hole, and your gear will be vastly different than what is used by wide stance squatters. If it isn‘t, it should be. The only caveat to this is health. Box squatting can be much easier on your knees than free squatting. If box squatting allows you to squat regularly without knee pain, do it! I‘d rather have you perform a squatting movement than no movement at all. It's paramount that your box squat form looks like your free squat form, gear or no gear. I've seen countless people take the ―sit back command way too seriously. Their shins are at an obtuse angle to their feet. Think about it this way—if someone were to take the box out from under you while you were sitting on it, you should be able to hold that position and squat out of it. Another thing I‘ve noticed is that people relax too much on the box. I think this is a horrible idea. Even when wearing gear, you should never relax your body. Stay extremely tight throughout the entire movement. Don't relax anything.