(Edited because I have more info!)
To answer one of your points; The ZEXAL person investigating KaibaCorp’s existence was Trey, in his own event! He was even asking Quattro “Hey what the actual hell is this” 😆😆😆
Also, the VRAINS characters themselves seem to be the real deal, given that from their perspective Duel Links is a deeper extension/alternate part of VRAINS that according to Blue Angel in her own event “Was not created by Sol Technologies”.
In Spectre’s event they even investigate how Duel Links can recreate entire events based on how people memorize it (For example, the threat to VRAINS’ existence from the Hanoi Tower or even the Lost Incident, which is absolutely insane!!!), which also explains how A.) The ZEXAL World is repeating events from the anime (Probably Don Thousand and the scattered Numbers somehow interfering with everyone’s memories again) and B.) Revived characters returning to their original viewpoints from before dying/recovering their memories (Examples: Yuto and Aporia’s revivals in their own events).
EDIT 1: Most characters themselves being AI can be corroborated by the fact that some have lines for both anime/manga cards, implying they’re a composite of the original character! (Example: Duel Links’ Jack is a composite AI version of the original 5Ds Jack, given he has lines for both his anime/manga 5Ds and ARC-V counterpart cards).
EDIT 2: Point A can also be proven by Jim’s event, in which he explains to Syrus and Hassleberry that Duels within Duel Links leave behind digital data similar to fossils which when unearthed can reveal memories (forgotten or not) and repeat them in real time (Again, we see this happen in Spectre’s event) (This would also explain how the ZEXAL cast remember more and more memories the longer they stay in Duel Links and duel there).
Duel Links lore is ABSOLUTELY INSANE once you start paying attention to it, and it would be hard if not impossible to keep up with all of it if it weren’t for the community and YugiTubers sharing some screenshots (shoutout to Veiz and YuDL!!!).
This is why regardless of metas or gachas I will always advocate for Duel Links to have a long lifespan. We needed something like this!!!
I'm sorry but WHAT is happening in Duel Links??
*CRACKS KNUCKLES* ALRIGHT im certain other people could explain this better than I could (bark at me if any of this is wrong,) but, an attempt at a quick rough tl;dr of it:
so like. an important thing to note with DL is that like..... the in-universe explanation for Duel Links is that it's one of Seto Kaiba's new VR Next Evolution of Dueling Ego Projects, which like, ok sure, he Makes Those, but what's a little alarming with this one is that technically (almost) none of the characters In The Game are actually Those Characters Specifically, they're AI recreations of them with their original self's memories (that's already a lot, right out the gate.) (I say "almost" everyone because I think it's implied DSOD Kaiba and maybe Mokuba actually Are them because it's Their Game and they're always product testing it, there might be others though)
anyway another thing with this situation is that, uh, Most Characters in Duel Links Do Not Know They're AI. They just assume they're the original guy, that's just them! Hanging out in this cool new Duel VR! But then sometimes you DO get characters who actively are aware that they're just code in a video game (Yami Bakura and Bruno 5D's both comment on it), so you have this really interesting ecosystem of duelists who Are aware they don't really exist, and duelists who are None the Wiser. absolutely batshit.
and sure this is all well and fine with like, DM and maybe GX characters, ok sure it makes sense Kaiba would be recreating notable duelists of that era, but i cannot stress enough He Is Also Making AI Recreations of Dead People. DL very much takes place post-manga, post-DSOD. But Yami Yugi is There. Yami Bakura and Yami Marik are Very There. Manga Pegasus is there. Seto "I Will Never Learn to Come to Terms With Grief" Kaiba is actively raising the dead in his little VR card game simulator so they can live forever and there's a 50/50 chance they'll be FULLY AWARE that they died. JESUS.
There's also the hulking elephant in the room of Duel Links Has Been Including Characters From Series Kaiba Has Nothing to Do With For Quite Some Time Now--and a lot of those characters are like HEY. WHERE THE FUCK ARE WE. like I SWEAR someone from either Zexal or Arv-V was actively like "hi what the hell is KaibaCorp" so like...Kaiba's branding is ALL OVER THE VR WORLD EVEN IN THE WORLDS HE DIDNT EXIST IN. It's painting this absolute off the rails picture of Seto Kaiba trying to create this virtual multiverse of The Best Duelists From Every Timeline Living or Dead, and half the guys he's pulling in at this point are like *spawns into a perfect recreation of their hometown with no real idea of who did this* "what in the goddamn."
like guys from zexal/arc-v are actively IN GAME like trying to figure out why this VR world exists and who created it. It's absolutely wild and fascinating to watch. excited to see what happens when they add VRAINS world next month?!?!? idk anything about VRAINS really but it's probably going to make the DL lore even more bananas.
ANYWAY. ALL OF THAT SAID. NOW WE HAVE MAXIMILLION PEGASUS DROPPING IN-GAME OMINOUS SENTIMENTS it's kind of a culmination of all of the aforementioned shit. Duel Links Pegasus (an AI recreation of manga!Pegasus, who is fully aware A.) that's he's dead and B.) that there's multiple worlds and timelines crammed into this Virtual Reality) has a conversation with Paradox (an AI recreation of Paradox the Bonds Beyond Time Yugioh Movie Bad Guy, who, for all intents and purposes, fully believes he's the real dude and he wants to kill-die-explode-murder Pegasus SO BAD) breaking down that "hey, this place unites different histories, and if you kill me duel monsters won't cease to exist. Anyway, I'm not real! Ohoho! This world holds threads of tragedy, Paradox-boy!" <-- (not verbatim. but i wish it was.) Meanwhile Paradox is having a sputtering breakdown right next to him. This is a video game to play yugioh the trading card game.
like. it's just absolutely wild. konami could have just said "hey heres yugioh characters from every series. whatever" but no instead they threw in a bunch of mild psychological horror and inter-series friction and existentialism and it's a freemium video game that i have 600+ hours on on steam. yugioh duel links !