I'm sorry you're confused! The ending is purposefully ambiguous, so I don't want to get my authorial intent all over you - it's really up to you to decide what happened with Leela and the TARDIS. I will say that I think the Doctor is probably overreacting because Leela's apparently driving the TARDIS unsupervised, just like he shouted at her in the beginning of the fic/the last scene in The Face of Evil.