The 3900 m2 area proposed in the competition brief refers to the total usable area. If you add up all the areas for the classes, workshops, dorms, cafeteria, etc. 3900 m2 is what you get. If you decide to lay everything on a single floor then that will also be your building footprint, however if you choose to create multiple floors then your building’s footprint will be less.
As for what we mean by “challenge the suggested spaces and dimensions”, I’m going to refer you to the question asked by Sarah a few days ago, as I believe there is a good explanation there https://arkitekturo.com/topic/question-on-the-brief-project-to-imagine/
Please let us know if this does not answer your questions of if you have any other 😉