I think SADunbar is right; The most critical points to measure should be the swing arm pivot mount pads (those 1-3/8 holes, NOT the swing arm pivot bolt) and the steering neck.
These would have to be the most tightly controlled aspects in manufacture. You'd have to assume that the tolerances for the relationship between these points would be the tightest on the entire frame. The exact location of the holes drilled for the engine guard mount and the rear frame extension would certainly not be treated as critically.
You'd have to imagine that the frame is built on a jig starting with on these three points.
A true measurement of the steering head's angle and orientation would probably require full removal of the fork.
Was the frame perfectly level side-to-side during the 'plumbing'?
I can't guess how the dealer determines whether a frame is officially bent but I would expect some sort of jig or gauge.
As an aside on a point repeated elsewhere... the dealer doesn't determine whether the bike is a "total", only the insurance company will determine that. The dealer has influence, of course, in estimating repair costs and deciding what needs to be included, but they don't actually get to tell the insurance company "you have to total this". The owner also can't make that decision; he can request, negotiate, make noise about it or take 'em to court.
The insurance company has the money and (barring court decisions) THEY ultimately decide how to use it.