The option was offered to select a name for yourself in earlier versions, as in a name that you would have post-Transition. I understand removing a few choices with a retcon (like the vending machine in Ch. 1) but removing the choice of a former name felt a bit odd.
It's because Isaac can no longer be classified as an audience self-insert. Arguably, he never was. The original intent was to let players fully immerse themselves in his situation by letting them choose his name both pre and post Transition, but since he's got a defined personality, backstory and storyline, it's far better to give him a clearly defined pre-Transition name also.