I'm not a website judge, but my opinion is that some degree of customization is intrinsically necessary for any project to succeed. Practically nothing can be made from 100% COTS parts, save Vex or LEGO robots. In FRC, every team uses customized parts to some various degree, whether it's everything but the shifting transmissions, or only the arm and manipulator on their robot. But the fact remains that at the core, every team uses COTS parts.
Yes, a team
can used to be able to built a robot using nothing but Kit parts, but if you wanted to do anything other than drive around you needed some degree of customization.
For team websites, there will always be a need to customize things. Sometimes the solution is to write code yourself, other times it's to use as many open-source technologies as possible to create a wonderful end result. There is no shame in using widely available open-source CMS systems for your website. Even
www.whitehouse.gov uses
Joomla Drupal.
Customize graphics. Figure out how the engine works and create a custom page layout theme. Figure out how to extend it. Do something to change it. Add content to it. Lots of content. And as long as the end result shows obvious changes from the COTS code to better reflect your team's goals, then in my non-official opinion, I'd consider that in the spirit of the student-coded goals.
Disclaimer: Back in high school I wrote a CMS [still] in use for Team 228. Starting with PHPBB for the forums, private messaging, and unified site login, I wrote all the code for the non-forum CMS features (like the photo galleries, news articles, event calendars, media tag clouds, content caching system, etc) and did all the graphics and content work myself. It took (on average) several hours of work every day for three years to do everything.