It's not supposed to play a role in the appearance score, but I think it does depending on the judge.
Quick story: I took Tuffy Stone's competition class a few years ago, and one of the other students was a KCBS Master Judge. So when discussing some of the things Tuffy would ask this gentlemen how the judges perceived it, and how they would score, and things of that nature. When talking about garnish the guy went into a long rant about "wanting to see that the pitmasters put some time into it." He said that if the garnish wasn't aligned properly or if it was sticking up in one place that would usually end up with a small deduction. He also said that if cooks did something like putting a flat piece of lettuce on the bottom that would also receive a deduction.
Mind you this guy was a Master Judge and this is what he's saying about his judging process...even though it clearly goes against the KCBS guidelines. Again, this is a single case and it's all hearsay as I'm just repeating what someone else said, but I figured it's worthy of discussion.
Personally I'd love to get rid of garnish as I hate paying the extra $10-15 just so I can stuff greens in a box. I know people are used to it and make use of it for keeping the meat in place in the box, but all the other organizations don't require it and people have figured out how to make it work without garnish. For me it just seems like an extra step that isn't necessary...and with the possibility of it actually being judged (at least in some capacity) it kind of really deals a blow to the newer teams who are trying to figure this stuff out.