Even more than the huge jump to the grim ending, I think it was the articles that sort of stood out to me. Especially before knowing the game's ending, reading about these very grim historical topics and events while watching cute pixel art guys ride stationary bikes to upbeat music was mildly off-putting, at least for me.
I will say, I don't think tonal dissonance is necessarily always a bad thing! In some ways it might work for you thematically to have those tonal shifts. Maybe, for example, creating that discomfort I felt while playing works in the game's favor once you're hit with that last link? Just some thoughts.
Your point about the time limit makes a lot of sense too. I can appreciate that for a jam, the scope of the story needed to stay small while still being able to tackle this larger topic.
Anyway, hopefully that helps! If you plan on working on this more after the jam, I'll totally check it out. Like I said, this one really works for me.