I know that Matt Smith's doctor thought his time ended, but there are even bigger plot holes that can't be ed for, namely the 'forever' companions...

Let's start with Clara... they explained that she showed up in every doctor's timeliness after she was splintered across time/his life. Wouldn't she know about the doctors after Capaldi's doctor? She is not only the impossible girl, she became immortal AND ran off in her own TARDIS with 'Me' a.k.a. Ashilda.

Which raises the question, we know from the end of the universe, as it was burning, that 'Me' was there not only waiting for the doctor, but knew of all his incarnations. Yet she treated 12 like the last! Wouldn't she know?

And then there's Captain Jack a.k a. The Face of Boe. Where's his knowledge/awareness? He was present during Whittaker's timeline.

As for this whole Timeless Child nonsense, the simplest explanation is that the Master lied to Whittaker/13. We've already seen where the Doctor on more than one occasion has been emotionally overwhelmed by his need for his counterpart, starting with Colin Baker in Trial of a Timelord to Tennent with Martha when the Master's wife shot him, to the strange relationship with Missy and Capaldi to Capaldi reckoning with Bill being turned into a Cyberman. It's not unreasonable to see how Whittaker would believe the Master's story of the Timeless Child.

Too many unanswered questions...