You are absolutely right about that mistake of just making a drastic correction of the offset by repositioning the wheel on the steering shaft. Usually that happens after major work where a lot of front end work is done, damage etc.
Not only can the left/right max lock to lock be off but the cancellation of the turn signal switch can be effected.
So Honda wants the rack and pinion gear to be in the center, steering wheel centered at the same time. In addition the steering shaft may also have to be centered if there are any mechanical functions on the shaft that depends on that.
Also of cause the toe in/toe out of the wheels also need to be in specification when the above is right, I guess most new cars are 0 but I cant find any info on the Clarity for that