I think Bonney is a clone.
Bonney stated that she was in Egghead when she was a kid and when it was still a normal lab and when Vegapunk was still only 1 person, so this might be implying that she was born on Egghead.
We know she is Kuma’s daughter (adopted/biological) and he has been heavily involved with Dr Vegapunk. Bonney could have met Kuma in the lab. She lived with him since then, as form of protection.
It explains why Bonney doesn’t have a mother and why she doesn’t even look like Kuma, not even a single word is said about her mom.
Also, Bonney has been sought out by the World government for unknown reasons.
Dr Vegapunk has had many inventions and one of them is to replicate Devil Fruits. He’s able to recreate Paramecia types by using the user’s lineage factors.
Bonney’s abilities so far have been related to time.
A key character entering this arc is one the highest ranking celestial dragons. And as confirmed by him, he once met Dr Vegapunk. 
Most importantly, his name is SATURN. Saturn is the roman equivalent of CRONOS. Cronos is known as ‘father time’.
Piecing all this together, Dr Vegapunk once met him to extract his lineage factor so his abilities can be recreated. Bonney’s Devil Fruit ability is a replica of Saint Jaygarcia Saturn.
