Chris, you're up early! Got cows to milk or something?
Anyway, to answer your question, where the body sits is irrelevant. All we are interested in is the chassis. Bear in mind Ron's initial question.
"I need to acquire some basic alignment skills. I have successfully measured toe and adjusted it at the track using borrowed toe plates, and made some eyeball camber changes as well. Too much time, and money, is spent dragging race cars around to alignment shops. I need to be able to check alignment, adjust after offs, and generally be able to make changes when I wish."
He is not talking about initial setup which is considerably more involved and time consuming and is probably easiest done at an alignment shop. For making adjustments those settings are already there and shouldn't change for all practical purposes. After damage at the track, there is usually not time to do a full setup, it is more a case of getting the wheels pointing in approximately the right direction as quickly as possible.
A full initial setup is perfectly capable of being done by stringline and level, it's just that some measurements can be a little difficult to get. Bodywork in the way etc. For initial setup first you need to set your rideheight, then set the front track so that each pair of wheels is equidistant from the inboard pickup points on the chassis. I would use the upper point since the links are shorter. (If the chassis is is not 100%, and very few are it is better to put any differences into the longer lower arms) Then do the same for the rear. Then set the wheelbase so that it is the same for each side.
Then you have to check and adjust your diagonal measurements from an easily defined point on the uprights, then recheck your first measurements for wheelbase and track and adjust if necessary. When you are sure the car (wheels) is square then you go on to caster, camber and toe, as first posted. Not forgetting to check and minimize bumpsteer for initial setup.
Hope that brief explanation is of some help.
Then you go onto cornerweighting.......Ron posted a good link for this procedure in one of his posts last year.
Cheers,