I don't think you even need a detailed RAW explanation for why such-and-such a spell doesn't work (or why you should be able to break out of the main plot by level 3): it doesn't work because that's what the game says. My first experience of GMing was the Wildemount module Frozen Sick, and in the introduction text the players are told that there's a mysterious disease going round and none of the local clerics were able to cure it. The players all accepted it: this disease can't be cured by standard magic. If any of them had sat there going "but why doesn't Remove Curse fix it?!" all session, I wouldn't have bothered to run the game.
To be clear, there is no detailed RAW explanation in this case, since the spell would in fact work perfectly. As to the broader point - most serious, official modules, as well as most serious homemade campaigns in the world of DND, have always adhered to some modicum of consistent internal logic. That's not only true of DND campaigns, but of books and movies too - plotholes and contradictions are generally off-putting to most discerning viewers, unless intentionally done in a goofy setting.
Dealing with the query of 'Why wouldn't this thing which makes sense solve X problem?' with 'Because I said so' is just bad DM'ing, and trying to shift the blame to the player is even worse DM'ing. I've also DM'd for years and dealt with thousands of 'clever loophole/solution' attempts, or 'Gotcha' attempts if you want to present it in the worst possible light, although trying to have those moments of brilliance is half the fun of DND and why DND mechanics exist to begin with as opposed to just being pure narration, and I never had to answer in that manner. Either I constructed my internal logic well enough, or a player did discover a quick way to solve something, and then I'd adapt the story to their success and not the other way around.
It's not that hard. In your example, if you're aiming for that kind of disease, you could just plan the lore around it in advance - It comes from freaking Ao, it's embedded in the Shadoweave and can't be accessed through Mystran arcane magic, it's not a 'curse' anyway, and the list goes on. It doesn't take much, you don't even need COMPLEX lore, you could just make up a 'catch-all' excuse if you're lazy, but having an origin and story and background and logic that actually ties in to why it can't be cured by conventional means, even the most banal explanation, only makes things more interesting and increases immersion.
Back to the topic at hand, you could simply reveal that the Absolute has also screwed up your soul in some fashion and that eliminates all the resurrection options on the spot. That's what the actual DND books and campaigns themselves do too in similar circumstances, by the way, and all of them are designed with almost every possibility in mind because that's the mark of a detailed high-effort campaign. But the one thing we can agree on is that it's far less egregious in a video game due to its far more linear nature and it only being 'loosely inspired' by the spells and rules of tabletop. Still, given that Reincarnate circumvents the main plot itself just by casting it without any genius combos or multi-step methods, I do believe that Larian simply forgot about it.
