MTG doesn't matter that much. It's not related to this game really. MTG just used this game as inspiration recently. I wouldn't expect it to necessarily include everything. It's just a bunch of cards isn't it?
That's because it literally changes every expansion, and sometimes within the expansion. From SE's perspective, and probably a lot of MMO's perspective, or even games with DLC generally, each pack is sort of like a "new game" and a fresh arc of sorts. Yes, they advertised Endwalker as the end of a story arc but really each individual story was an arc within that, with its own main antagonist: Gaius, Thordan, Zenos, Hades, Meition/Endsinger, Spheen
Of course we had plenty of secondary antagonists in the background, but they weren't exactly the last boss: Lahabrea, Livia, Elidibus, Nidhogg, Fordola, Tsukuyomi, Vauthry, Hermes, Zoraal Ja
If we include patches, we could maybe also say: Iceheart, Ilberd, Golbez
And many others in sidequests such as raids, and those are antagonists of their respective sidequests, such as the Bahamut, the Goblins, Omega, Mitron, Athena and all our Arcadion "feuds".
