Probably dedicated hardware and more of a real-time operating system, that is, it played visuals and music perfectly frame by frame while emulators can't keep up / end up desyncing because ????. It's probably due to the dedicated (sound) hardware / chips. or something.
And, so the GFs have caused them to forget the orphanage stuff, but then once reminded of it, they all remember it just fine and seem to continue remembering it. So are the GFs harming their memories or not?
I think for me it's not so problematic that this was the direction nor even how it was unveiled. It's just kind of annoying that the plot point raises implications and questions that it isn't concerned with ever addressing again.
I remember playing the game at the age of 13 and thinking that it was going to have a bittersweet ending where they succeed in saving the world, but at the cost of completely losing their memories of one another.