I don't think the Tardis is actually the one driving all the time. There are just times when it feels like there is something it needs to bring to the Doctor's attention, or when it resists what the Doctor is trying to do, and so it can take control. And there are other times when it's either in full agreement with the Doctor's intentions, or doesn't care enough to interfere either way. I'd call it a symbiotic relationship rather than either one being in charge full-time.
Bringing it back to your intro to the thread, it wasn't the Tardis piloting itself in "Listen" when the Doctor was unconscious - it was Clara guiding it by using the telepathic circuits. The cloister bell was because the Tardis was about to cross the Doctor's own timeline in a pretty major fashion, thanks to Clara's distraction worrying about the Doctor while she was stuck into the telepathic circuits. But the Tardis is pretty accustomed to Clara fucking about in the Doctor's timeline by this point (that's what it picking on Clara in 7B was about) so it let her get away with it anyway.
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Bringing it back to your intro to the thread, it wasn't the Tardis piloting itself in "Listen" when the Doctor was unconscious - it was Clara guiding it by using the telepathic circuits. The cloister bell was because the Tardis was about to cross the Doctor's own timeline in a pretty major fashion, thanks to Clara's distraction worrying about the Doctor while she was stuck into the telepathic circuits. But the Tardis is pretty accustomed to Clara fucking about in the Doctor's timeline by this point (that's what it picking on Clara in 7B was about) so it let her get away with it anyway.
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