Poppy is “The Timeless child” Throughout the history of Dr. Who we have been given clues and The reality War put them all together.
1. The doctor has said many times that He was human on his mother’s side.
2. In the episode “The timeless child” They showed a black child being found by Tecteun at a portal and was used to give the Gallifreyans the power of Regeneration.
3 In “The story and The Engine” There was no reason for Poppy to appear unless it was a clue to the origin of the Doctor.
The Doctor is a physical manifestation of Infinity he was his own beginning, his own father, although as a time lord he was supposed to be sterile In the episode “Wish World” I believe he subconsciously whished Poppy to be his daughter, before he ended all the wishes.