Board Thread:Support Requests - Designing Your Wikia/@comment-8117023-20141012141559/@comment-452-20141013010833

Yes. Wikia Staff can quote that paragraph to forbid every customization because the "proper functioning" of the "user interface" is the default look. That's the paragraph they quoted to me when they told me that the top Wikia bar was not allowed to have a background image, and that links are not allowed to be added to the "On The Wiki" tab. (Although I notice that the Runescape wiki still adds links - shh, don't tell Wikia Staff.)

However, there is a difference between "technically against the TOU due to that paragraph", and "permitted by Wikia Staff".

tardis.wikia is a wiki that is both highly customized, and has worked closely with Wikia Staff, so the fact that those customisations are allowed on tardis.wikia means that Wikia Staff have not forbidden them.