It's also bound to confuse long time viewers. We saw Hartnell's 1st Doctor steal the TARDIS and run away in it. So did the Timeless McGuffin steal a TARDIS, run away in it, and start calling herself the Doctor, then somehow get captured by the Gallifreyans, get her mind wiped... and then they let her/him do it again later? Are the Gallifreyans truly that mind-bendingly stupid?
A further thought: every backstory on the relationship between the Master and the Doctor at least in NuWho is that they grew up together. How did they grow up together if the Doctor is the Timeless McGuffin?
True, we saw River Song go from a teenage/young adult Melody Pond to a little girl in an alley after she regenerated. But River Song is just another bullet in the Timeless McGuffin story, because she had the regeneration ability and wasn't Gallifreyan. She inherited it by being conceived on the TARDIS or whatever, so it's not a species-exclusive genetic trait but an environmental one. Conceived near a time vortex? Regeneration, whether Gallifreyan or just bum-average human.
It's also more than possible that the Doctor didn't remember the "Ruth" Doctor, because "Ruth" was not the Doctor at all. We only have her word for that being who she is. Her callousness about death? Her being a fugitive? Could entirely be that "Ruth" was actually a future incarnation of the Master.