"But what to make of the Doctor’s meltdown in the TARDIS? This was a unexpected moment, his console trashing made more powerful for its silence over swelling music. Why now, looking at harmless blank space, having survived death on may occasions?"
Gavin, he wasn't looking out at harmless blank space when he visited the Gallifrey coordinates the Master gave him. Go watch the scene again - there's a very good reason for his flip-out.