You might be right, but if so it kind of fell flat for me. I don't know if you can actually have a commentary on existentialism and the authenticity of the self in a five-minute-before-the-end twist and wrap that in a killing game with shit motives because sequelitis is the death of creativity. That might be the big issue with the theming in this game : everything being clumsily crammed in the final chapter. Like you said, too many balls being juggled.
I think it really depends on whether you feel the meta-fictional twist, and everything that falls out of that, are properly related to the truth/lies, reality/fiction thematicism. I'd be willing to argue that on some level it does; the DR of the 'outside world', where DR is constantly repeated out of sadistic voyuerism and cheap affirmation without any meaning, denies the reality of the pain it inflicts on the participants. And I think the DR of the outside world sort of speaks to Kodaka's outlook on what making DRs ad naseum would be like, from his perspective as a creator; that continuing to create characters through all this suffering again and again to always come to the conclusion that 'hope will always triumph' or whatever would make those games lies, because the reality is their suffering *would* be meaningless, their 'hope' eternally fleeting. For DR to have any sort of truth, there has to be a finality to it.
This doesn't invalidate DR1/2's message, it in fact respects what they were doing by maintaining their uniqueness. The DR of V3's outside world is a perverse joke where 'hope and despair' are hoary phrases divorced from any meaning. So forcing the game to end, the victories of those distinct narratives can have meaning. Fiction isn't just made to be consumed, but can have a qualia of truth that makes the act of creating and experiencing something even as silly as Danganronpa worthwhile, but that can only exist when the act of creating and experiencing are done in good faith, not out of mere familiarity or obligation. I think in that sense the arbitrary way Hope V. Despair suddenly is interjected into the narrative in Chapter 5 is a clue in to the final twist; that a story where the outline of narrative beats to his known from the outset isn't worth telling.
The broader question is, could you accomplish this all without the metafictional twist? Well... I dunno, but I think for Kodaka it was sort of necessary to ensure that the earth was salted with DR; that there could be no pretense of their being a 'legitimate' Danganronpa game after this one. He's said his peace, and he's out.
The meta fictional reveal wasn't planned at all. It only happened because Keebo broke. When she says they're still "on script" she means that she's confident they won't end the killing game even though things have gone completely out of hand. If he didn't break they probably would have gotten another flashback light to make them think that like Maki was secretly a remnant of despair too, or for her to remember a time when Kaito told her she could avenge his death by killing Shuichi or something. If you remember, during Chapter 6 investigation Tsugumi just lets you find the Kaede's sister false flag and tries to trick you into thinking she can't get Motherkuma to do anything. She for sure wanted the Hope's Peak motivations and killing game to continue.
She wouldn't have placed the History of Hope's Peak Book, knowing it contradicts their flashback light memories,
unless she intended them to uncover it. The way she goes about the final trial seems to imply that the revelation of their fictional status was the way of inflicting an ultimate despair on them. All the stuff beforehand could just be part of her showmanship; it's totally a DR tradition for character's to divert from the truth merely as a way of ratcheting up the drama, which is definitely Tsumugi's modus operandi in this case. wrt to the first case, it's already been established that the Masterminds can interfere with cases from the very beginning; see the bogus Trial 5/6 from Danganronpa 1.