Retcon

If you want to get technical about it, there are no plot holes in the story of the Doctor's life. Every change to their story, every time their origin changes, it's the correct version. We're talking about a being who can regenerate, and who does so in all kinds of different times and places. Each body goes running around in space and time changing things. Saving space babies. Stopping invasions. Making changes in points in time all over the universe. We know really well what stopping something from happening or accidentally starting something happening can make major changes, and aside from the Doctor and their companion, no one else notices the change.

So maybe the Doctor is half human in one instance, just an average Gallifreyan in another, or the origin of the Time Lords in another. They've met themselves repeatedly and occasionally remarked on their aging process. Elder Five can talk to Active Ten because in that instance, Five hadn't regenerated into Six yet.

I bet if all the regenerations sat down and tried to figure out their biography they would never be able to get it straightened out. Eleven could have done something and Three could have done the same thing so they both remember .... I don't know. Starting the Great Fire of London ... but it didn't happen to both of them at the same time.

Wibbly Wobbly.