Hi Calum,
Here's my take on the code issue. The code brief states:
This project is designed to mimic studio processes. It is important that for this challenge you utilize the existing project and do not start again from scratch.
Keyword there for me is utilize. They've given us some base mechanics and a base solution so build from that. In real studio processes code gets dropped all the time! My approach is if you can look at the final game, and can clearly see it's an evolution of the original code base, then that should be fine. For example, the mechanics of flocking/repelling are a huge part of what we were given, so that should probably be in the final product in some form.
Regarding build platform, I'd stick with desktop if I were you. Just my $0.02, but it's going to reduce any chances of causing problems. What if the judges don't have access to the hardware? Or they don't have a device with the specs to run your game well enough? Given our time-frame if I were you I'd stick to desktop and save yourself a myriad of potential headaches. Again, take that with a pinch of salt. 100% just my bias opinion on the matter. :)
Good luck dude! Hopefully someone from Aardvark will be along to clarify!
Dale