It's really only the incredibly brief pre-credits Clara scene that creates an issue here. Otherwise the Doctor could have regenerated into Hartnell on Earth, after nicking the TARDIS. And for a show that joyfully and regularly creates loose or even tongue-in-cheek explanations for things there are a million possibilities. Perhaps because Clara was in the Doctor's timeline she saw the Doctor as they saw themself at that point in the past, not realising they were the Fugitive Doctor. Indeed, although 'Fugitive" comes at least in part from the episode title she came from, it would be very apt if the Fugitive Doctor was the one to first steal the ship and flee....

Also, as the article suggests, the future of the show is more important than its recent past so it seems odd to bring this up now. Will Chibnall-bashing never go out of fashion? He stepped down literally years ago now.

(Edit - tbf there is an issue with different time periods with this theory... But hey, this is Nu-Who, we just say 'timey wimey' and that solves everything right?)