As much weird timeline bending as they've done, Bi-generation could possibly explain a lot. Remember when 2 met with the Brigadier in The Five Doctors? He clearly knew all about 3 and was talking shit about how he "was not too pleased with his replacement" as if he had already regenerated yet also somehow kept living as 2 for a bit. "I'm not exactly breaking the laws of time, but I am bending them a bit."