I spoke to the owner of an unrestored 60K mile SIV today.. (a car that atteneded many of the AU nationals) the car is smoonstone white, I will be gogin to take some pics on the weekend, but after a phone conversation today.. there is body coloured paint in the front guards under the underseal, there is body colour in the rear guards, though only lightly at the top of the well. The front area where the X frame meets the front rails (the ribbed zone) has a very good coat of paint.. interstingly enough there appears to be templete marks (similar to those used in the grill area to paint the black inside the grill openings) to stop the underseal gettign on the sills and the rear valence/sills.
In the front guards where the headlamp buckets are there has been a black finish applied, but better lighting when we check it out should give an idea.
This is a car with no hits, original paint, interior etc.. never been apart. There is also an autumn gold S3 being restored here at the moment, original owner doing first resto.. gold paint on the body under the stone finish.
There may be some inconsistancies on the order of which the finishes were applied, and may have changed suring production but there are definatly cars with the paint on in the gards and some way into the underside.
As a side note the SIV has original rubber plugs (original sealer removed from top of them during the strip down.. this was a surprise as many will now there were also srung metal plugs used to fill the pressing holes in the fllors, boot, rear deck.. yet there are cars later and earlier that have metal and some have rubber.
Also steven.. as you would note from the STOC board where you posed the question a few members agreed with you.. and one member who did also pointed out a guy who restores the cars had pointed out to him that he had seen the cars with the paint in the gards/body as well.