Or it's the same diner and they forgot what side of the road they were on the "first" time.
Or it was a TARDIS both times, and it moved to the other side of the hill.
Did they actually confirm if the Doctor was "half human on his mother's side"?
More like a funny suggestion than anything. I doubt it'll ever be totally confirmed.
These excessively long lifespans do worry me. Ashilder survived billions of years since the last time she saw the doctor and clara, but remembered who they were, and had so little going on in the previous thousands of billions of years that her interactions with them would still be "noteworthy" in her indestructible library? During all that time she never once managed to get buried underground like Jack was, or caught on an exploding space ship, or ran out of fuel on a day-trip to Pluto and ended up on a galactic escape trajectory?
Even the Face of Boe died. In 5 billion AD. The end of the universe is 100 Trillion years after that.
This is definitely a case where you have to suspend your disbelief. "Even the other immortals have gone," she says. I wonder how long she's been completely alone.
Although who knows? Given the events of "Face the Raven," she obviously had contact with the Time Lords who were hiding at the end of the universe. Maybe she didn't actually have to go "the long way round." She could have been living on Gallifrey that whole time, in which case she would have easy access to time travel.