Daniel, I've seen some internet scratch builds of "car models" done by machinists that looked cool but wouldn't hold up under judging at an IPMS event. Most of the items looked clunky and out of scale. Is that the point your making?
A few years ago I saw a 1/16th scale Fokker D8 in the bones that was totally scratched from plastic sheet and rod. It was stunning and it won the show. I believe last year the Nationals winner was a scratch built Mercury or Gemini stack.
Just before our Austin show last year, a senior member of my club made the point to the judges that scratch built is a separate category but must be totally scratch built, 100%. Partially scratch built models go in their respective category with the other detailed kit models. (EDIT: I just glanced at the 2011 Nationals categories and notice they use the words "scratch-built and conversions" for automotive)
I haven't ever seen more than one scratch built entered in the scratch category at a show but it's a rare builder that takes that path. Yes, each time they won their category. So what? They always won the show too! Nationals usually have multiple scratch-builds competing.
It's obvious how to win best auto or best ship. You make a near flawless example dripping with details. Winning a "Judges Best of Show" or JBS, is a different award however. That is the model judged from the group of "Best of" models that has the highest "Wow Factor". It might be an incredible paint job. It may be an expertly carved facial expression or something so complex it mesmerizes anyone that contemplates it.
Since the scratch category is by itself it gets a shot at "Best of". Then, after winning "Best of" it gets a shot at JBS. JBS really isn't about basic skills anymore though. That stuff gets stopped at the category level for most models. Those lonely scratch entries would get stopped at the "Best" threshold for poor workmanship.