how much can we customise theme?

We are new to wordpress and looking to build a knowledge base site for health information.

Its makes sense to us to use an existing theme such as flat base as most of the functionality done for us already.

http://themeforest.net/item/flatbase-a-responsive-knowledge-basewiki-theme/7264664?ref=athemez

We wish to make our own design without being confined too much by any existing structure while keeping the functionality. Question is, is this possible? I realise themes can be ‘re-skinned’ but we’re are talking about a complete redesign. Will it be lots of work and better off starting from scratch and building a custom theme?

(We also need to add a wiki style user edit feature to the theme.)

Thanks in advance!