Since I know this will be appreciated...
Below is a save file before the Convenience store you meet Niijima, but with the quest flag of you meeting him flagged.
The player spawns immediately before the upper road that normally is blocked off. The quest SAYS to go for the convenience store, but going north will be allowed, and you can continue the game alone.
Two things to note: This is poorly-tested. Niijima's dialogue in cutscenes still appears, so that works, but I'm unsure what would happen in the cabin. Use at own risk.
Secondly, if you go into the convenience store, the cutscene will trigger and Niijima will be added to your party. I think I looted everything before said store, but you will have to forgo the items within. ...Not that that's a problem, you need to TRY to lose this game...
To clarify, are you trying to report a bug, or are you providing a save file which allows you to bypass having Niijima for the rest of the game (for people who don't like him)?
If the latter, I'm assuming you hacked the game scripts to turn on the switch (23) that triggers when he enters your party, but without actually meeting him, and then created the save. And yes, it'll look rather silly since as you said, the text afterarrds (and the devs) already assume that you've already met him so you'll have his 'ghost' dialogue throughout the game. At the cabin, the game is scripted to remove Niijima from your party, unless you select my added branch, so I don't think it'd break anything not to have him there, other than Sally just talking to nobody (well, Niijima will respond in dialogue, but he won't actually be there).
However, in my added branch in the cabin, I've scripted that branch to remove and then add Niijima since his character avatar was impossible to move in cutscenes (given there's not enough room in the game map to have multiple iterations of his avatar in the exact same place for different branches). Therefore, even if you avoid using him the entire game with this hacked save, he'll suddenly appear in the cabin regardless, if you choose that route, and remain as your party member (and you'll also have that ending). Oh, and btw, IIRC, the switches I used to create the branches don't actually check if Niijima's in your party since he's originally intended to be in your party up until that point and unkillable as well, so I'm pretty sure you can trigger the route and not break anything.
If the former (and you're reporting an unintended bug), then I have absolutely no idea how that happened by accident.
