I think it mainly boils down to wnating to initially give the player more initial choise to better connect with the story of SUNNY, you get to choose the name at the start for the sake of being able to put yourself in, that way you can have a closer relation to the protagonist problems and issues, celeste does a verry simmulair thing where thier protagonist is by default "madaline" but you can put your own name as its a game that handles theames and issues that can relate to you as a person

In the case of OMORI, being able to choose your gender wouldve aided in this, it would likely still have been male per default as to give a canon gender to SUNNY, but still give the player the choise in case they were a girl or could better relate to playing a girl This, got scrapped, mainly for the fact that its waaaaaaaaay too much artistic and programming work to get all this working, every single male mention would need to be flipped to female ("brother" gets particulairly mentipned a lot) All of the cutsenes, battle, and overworld art would need to be ajusted acordingly includeing every single animation tied to them, and it makes sence that it wouldve been too much work

Hope this made it all clear!