I hope this doesn't come off as too uninformed, but when Nier Becomes the Original Gestalt in the Prologue, is it assumed that what we are playing as the Replicant and not the Gestalt during the remainder of the sequence?

Which makes me wonder where and how the Original Gestalt was able to come into the picture, whether or not he ever met the Replicant Nier during the time of Project Gestalt, and if the information scientists explained was brought to his attention alone, or Replicant Nier 0 (Prologue Nier) as well, plus where or how both Yonah and Replicant Yonah were present. I guess it's more of a weird situation on my part as digging has resulted in nothing on these very specific questions. Thanks in advance for any more lore-savvy folks.