Maybe you’re better at ferreting than me. I’d goggled “Transistor ending” and only seemed to find discussion of ng+. Between that and the reviews I found, it didn’t seem like anyone was critiquing her suicide/leaving the world destroyed.
I didn’t completely understand how 999 worked the first time I played it. I got about as good an ending as possible on a first playthrough, but that still left some major questions unanswered. It was a couple months before I read something about how the multiple playthroughs worked and decided to go back and finish it.
I’m not sure this is the same thing but I got one of the early game overs in Super Paper Mario through dialogue choices (The one where on of the bad guy’s henchmen asks you to join him but instead he takes over your bodies ending Mario’s story I guess) and never bothered finishing it because it put my back to an earlier save. The game wasn’t that great anyway so I don’t really regret missing out on a few boss fights.
Also I think I got one of the endgame optional bosses down to like 1 hp and died… that game hates me.