I'm the dev, so you might not think I'm the best person to answer this, but I believe it's totally fine to play the base version of the game. All the extra scenes have no bearing on the story, and are mostly meant to involve extra characters that aren't all that relevant to the story.
I can assure you that playing the game without the extra scenes makes perfect sense, and the scenes are incorporated in a way that if you don't know they exist, you would never notice there's supposed to be extra content. This time, I made the mistake to keep the door to the extra scenes in the reminiscence room, but I usually never do that, because it feels like I'm just rubbing the extra content in people's face, and I hate doing that.