If you read the dialogue throughout the game, NLT explains this.
To my understanding:
Sofia/Nadia and Alia/Zyana (spelling) were both kept at the age they were when they were trapped/hidden through the benefits provided by the FoY. This was centuries ago, as Alia was a child at that time, and Sofia a bit younger but likely not that much (as she left the cave to become a treasure hunter when Alia was lost and kept returning to harness the FoY's benefits to maintain her youthfulness).
When the flood swept Alia away as an infant, she was rescued by Sam and Naomi, adopted and grew up without knowledge of her past but also able to develop "naturally". There's little scraps of information dotted around everyone, it's about joining them that may be tricky.