Saying that everything contradicts is a very broad statement. The adaptions don't contradict the "history" that is told in the story. The Charrl still send something to London, Spring Heel Jack is still involved. Benny is still stuck on Guernsey and Jason merely takes Chris' role with a little bit of the Doctor's.
As I and Cult Of Skaro have said cover everything and if it contradicts the novel takes precedence, just as we do the novelisations.
The contradictions in these adaptions aren't any more difficult than any of the other contradictions we're presented with in our valid sources, they're just easier to be suggested to be excluded from what we cover than any of the other stories.