Most of my opinions have been drawn on posts on outlaws, and my own experience with block periodization and volume training.
The box does provide an artificial bottom to the lift for a raw lifter. Modern gear is strong enough that it is almost like a box to bounce off of when the straps are up. Raw lifters do not have this feeling. I think it CAN be a useful tool but is far less useful for a raw lifter. Too much use for anyone will create instability in the hole if you are used to having a box to sit on rather than stabilizing and reversing in the hole. The raw guys I train with NEVER do box squats anymore, because they just were not getting carryover from it.
Even some of my multiply training partners are shying away from box squats now. They are definitely a tool and if they work for you then do it. Everyone is different and all of this is basically just different training theories.
There are differences between raw and geared training though.
It is my personal belief that volume work is more effective for raw training. Max Effort should be worked in, but not constant. Remember gear provides protection, and when I have done westside raw I have been terribly beat up in just a few weeks.
Beyond that your form, the volume you can handle, the CNS taxing, ect all changes when you go from raw to geared or vice versa. As far as leverages those change some too, but proper form should allow you to confidently go full range of motion. Of course cutting a rep short makes it easier so some people cheat, but I don't think that is due to leverages, just due to moving the weight further and people wanting to avoid weaknesses.
I stuck with a pretty strict westside template for years and made great gains at first, then stalled out. I took the speed work out and replaced it with volume for a few months and my lifts skyrocketed. I now only work speed work in 3 weeks at a time, and have made continual, fast gains. In a one year span like this I added 255lbs to my squat, granted I was gaining weight but still.
As far as bench/deadlift training, with just a 460 bench and 565 deadlift I suck at those, so I will not even begin to say I know how to train those. I have made some fast progress lately with raw volume work though, and look forward to big PRs when I max soon.
In my opinion there are people westside works for, regardless of raw/geared/ect... one of my friends is by far the best raw lifter in the state, and he is strict westside. Every week is max effort work one day, and speed work the other day. He is the most explosive person I have ever met.
I don't think he ever deloads either. I was convinced he was just a freak since he has a FAST 740 raw squat.
I would like to hear your feedback on westside for raw. Maybe my problem when I tried that was using too much band and chain tension to get carryover to raw.
I would like to add that in general I just seem to respond better to volume anyway. In gear I seem to do better with doubles and triples as opposed to singles. So perhaps my personal observations have been biased significantly by what has worked for me.