No, it's quite clear that changing the spells on an NPC caster for the same class spells and same level of spell = same CR and thus same XP. On the other hand, I'm kinda thinking that perhaps that line about swapping spells was ALSO written before they changed thedesign paradigm on 9th level spells.
This is why you have a DM who knows what they're doing. This isn't
Magic the Gathering or
League of Legends or Professional Baseball. It's not a competitive game where the DM is looking to maximize the damage output of his creatures, knowing that the party will be insta-killed by the CR 12 opponent. It's a story-telling and role-playing game where the job of the DM is to craft an enjoyable experience for her or his players.
Here are a bunch of other things that are also "quite clear" using the rules:
1) A dozen CR 2 intellect devourers should be absolutely no match for a 20th level barbarian PC, so the player has no excuses for not being able to handle them.
2) Every enemy wizard should always use the
contagion spell, and they should always select the one disease that applies a stun-lock to the target when they're damaged.
3) Monsters should always take the time to coup a dropped opponent. Every creature with an 8+ Intelligence knows about healing spells. Don't even give the cleric a chance.
Now, all of these things could be "balanced" out of the rules. But I don't want to see any of them vanish. Sometimes, a DM needs that low CR creature that freaks out the most powerful fighter in the land. Sometimes he needs the enemy wizard to use a stun-lock disease to create tension in a battle, whereas other times he needs a different type of disease to craft a compelling story. Sometimes he wants to use the threat of the coup-de-grace in battle to create tension; sometimes he wants to actually carry through on it to force the party to consider options for
revivify or
raise dead.
Meteor swarm is exactly the same. It's ridiculous to suggest that there's no change to the CR of an archmage by swapping in that spell. 40d6 will wipe out a 10th level party in a heartbeat. However, that doesn't need to be codified in the rules. There's a valuable place for a 9th level spell of that power, so it shouldn't be nerfed for damage. The current CR 12 archmage write-up seems okay, given the listed spells (so, no need to change the CR).
The DM decides whether, for story reasons, he wants the archmage to have a
meteor swarm. if he does, the DM should have a legitimate reason for doing so: either it's going to be cast on a non-PC target to scare the party, or the intent is that an intelligent party should be able to survive or avoid it (they've quested for the
amulet of meteor protection, or they have an
anti-magic shell, or similar), or maybe the story purpose is to kill the party... then run the next few sessions for their ghosts as they heroically seek to escape the Lands of the Dead... and return for vengeance against the wizard that killed them!
As a final comment: this point isn't restricted to
meteor swarm. It's about how you run the game in general. If you know the party can't handle a
meteor swarm and it'll simply end the campaign, don't use that spell. If the party is all non-casters, don't use
forcecage or
wall of force. If the party has no missile options beyond 30' range, don't use flying manticores. If the players have all decided on Charisma-challenged meat-heads, don't force them to play a political campaign where every failed skill check could result in their execution.
As a
player option,
meteor swarm is fine. It's the ultimate expression of pure magical damage output. It's not out-of-line with other classes. It feels suitably epic.