Well, the squats as used in the WOD are there to help strengthen the recovery of the clean and snatch, so they have a pretty specific purpose. Box-squats, if done correctly, are more for strengthening the hamstring/glute and working starting strength, which could definitely have some carry-over, but would probably help more on your first pull and your deadlifts, not necessarily the squat that you'd be hitting during the classic lifts.
If perhaps hamstring and glute strength, as well as "coming out of the hole" especially when you lose momentum, is your main weakness, they could be of use, and perhaps they differ enough technically from the high-bar Olympic squat that they wouldn't have too much negative carry-over. I don't know about using them instead of squats, but maybe throwing them in as technique work, like the tall snatch/clean etc., and using speed sets to specifically work the explosiveness of those muscles might be of use...but then you're getting into perhaps making everything more complicated than it has to be.
Any other thoughts from the more-knowledgeable around here? I got some great gains in my low-bar squats doing a WSB approach to the Crossfit Total for the month and a half before switching to the WOD here, and perhaps that (along with the good-mornings, Dimmel Deadlifts, SLDL's, Glute-Ham raises) helped form a good base of strength for the improvements in my pulls. One thing I know for sure, "building the lifts" from different movements tends to lead to workouts that are entirely too long for me, so I'm welcoming the simplicity of forgoing so much variety
But maybe that's just me!