It all depends on HOW you train, not the actual exercise. Train off a low box with a close stance and your raw squat will go up. Personally, I have not done a free squat since I tore my hamstring in April. Yesterday was the first time I have gone heavy and smoked a 605 raw squat with 140lbs of chain. Thats a 5lb PR on the weight and I had the cahins set much higher than usual.
Also, it depends when you use it in your training. If you are going geared, use the box all the way up to the meet. If raw, drop it a few weeks out for your hravy lifting. I really think speed work should always be done on a box just because you recover much faster from them compared to a super high volume of free squats.
Like I said before, I do at least 60% of my heavy squatting off a box and still make decent progress on my raw and geared squats.
It's hard to give actual reccommendations on what to do. Everyone has different levers, weaknesses, recovery abilities, etc. If I could just free squat all of the time and still get strong I would do it but that is just not the case for me anymore.