The whole thing is confusing, IMO. And everything with suspension is dependant on something else or a compromise with something else.
The SFC's just keep the front of the car from twisting separate of the rear and makes it act as a single unit (mostly)
If your car is "bent" there really isn't anything you can do about it now. If the doors open and the hatch fits, it is pretty good.
The goal is to lock the chassis down so it doesn't twist any more.
After you accomplish that, then set the corner weights. The end goal here is for there to be an equal amount of weight on the lf/rr as there is on the rf/lr and the tires can't tell the difference if the body is level in order to obtain that.
The torque boxes may cause a problem with the overall alignment of the car, especially the thrust angle which should also be corrected. You would want to do this before corner weight as part of correcting the alignment.
Unless your chassis is really tweaked, I would guess that proper corner weights are going to coincide with a mostly level body and all will be good. A 1/4" is a lot of corner weight adjustment, but would be hard to see from fender to fender.
The car is "straight" when all 4 wheels point in the proper direction at the same time and the lf/rr weight equals the rf/lr. The body may or may not be looking straight at the same time, but that is not relevant.