That's a curious claim. I think you mean "that's not how MM-style NPCs are designed", which is nearly tautological. But the rules for PHB-style NPCs came out first, in the PHB, way before the MM was published. The PHB gives rules for creating "characters", some of which are PCs and some of which are NPCs. The MM just came along later with a simpler form of NPC template, for cases where you want that.
Anyway, if you want a level 20+ NPC, you have two options:
(1) Make him level 20 with a bunch of epic boons; or
(2) Make something up.
You can formalize #2 by writing explicit rules for advancement beyond 20th level (I have) or you can just slap on whatever you feel like (e.g. proficiency in every save, legendary resistance), using basically the MM methodology. Which one you choose probably depends on whether you want your Acererak to be a passive force in the campaign (shows up for the "boss fight" and dies to the PCs in glorious combat) or an active force moving pieces behind the scenes and fighting intelligently. If the latter, you probably want him to be a real NPC with real motivations and capabilities, doing things that PCs could at least in theory do, and it's probably worth thinking up at least some rough rules for how you want characters beyond level 20 to function. E.g. does concentration work differently for them? Do they gain extra save proficiencies? How is his big evil plan going to work, mechanically speaking?
Depends on your purpose. If the NPC is designed to be fought by the PCs then you need to make that NOc using the DMG guidelines, because a level 20 NPC is more like CR10 to CR13, depending.
For example a level 20 Wizard could easily die against a level 10 party if he rolled poorly in initiative without so much as getting a spell off. With 150HP and about 40DPR or so that wizard isn't much of a challenge for anything but low level groups. The "archmage" in the monsters manual is what, CR12, and that's pretty generous.
If the NPC is not for combat against the party then there's very little point even bothering with stats.
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