These are then judged by the Food Instutute using the same criteria that is used in the final judging and they send the top 12 to 16 over to Bays. More testing and more judging finally gets to the six finalists. I know some years they allowed a lot of cubed, ground, etc. Unless the criteria for judging says specifically that you should showcase the muffin, I don't think it would make any difference. If you've come up with a great recipe using a cubed muffin instead of using it in the standard way I certainly don't think that would be held against you, except, of course, if that was specified otherwise in the criteria.
Presentation is very important.
Even if presentation or appearance is not mentioned in the official judging criteria you should assume that presentation can be critical. Just think if you were a judge and out came this dish that looked like it was dropped off a 10 story building. Lets just say it wouldn't help. Its a matter of getting the judges attention in a postive way. Something that was just average might do better in overall scoring if it was presented in a very attractive way.