Just taking a break from work right now so I'll try to be concise... because that always works out...
Anyway - some reasons:
1) RFD of the power clean is much closer to driving off the line than speed box squats.
2) Coordination demands of the power clean are much more complex. This is a good thing-football players need to be able to handle complex motor patterns and adapt to unconventional circumstances.
3) Catching the bar on the shoulders is a great aspect of the clean. An athlete isn't just dealing with a bar on his back - the force he's dealing with is actively pushing against him and there's a moment of impact, if you will, when contact is made. You need to be able to absorb this force. Box squats don't develop this.
4) Cleans are more explosive and demonstrate/develop more power.
5) Deactivating the hip flexors in a leg-dominant movement in order to break the kinetic chain is idiotic for an athlete. Not only is it unnecessary, but if the athlete gets in the habit, it becomes dangerous and injury could quickly result.
6) Bands and chains don't develop power as well as the Westside folks think. (there are a few papers/studies being written as yet unpublished that discuss this)They don't make up for the difference WRT cleans, and they alter the force production curve detrimentally. The athlete learns to produce force quickly in an improper manner due to a different learned pattern of excitation.
7) The grip component. Athletes need a strong grip, and cleans add to that as an economy of training time improvement.
8) Triple extension. You don't get up on your calves in a speed squat, but you do on the field. That needs to be included when developing/learning how to display power or, again, the movement pattern will be screwed royally.
9) Set-up time. It's a pain in the ass to set up bands and chains and takes a lot of time; if you have it, great. But for most it causes the workout to go beyond optimal length. It's a lot easier to just load some plates on a bar and clean it.
That's all I can think of for right now. Gotta get back to work...