Except it isn't. This is an XOR condition, you either increase the CR because of elite stats or because of adding class levels. Trying to paraphrase it more correctly:Um, no. You need to reread.
I said, "Note that the elite array, in itself, doesn't increase the CR; it's a side benefit of the class levels, which do increase the CR."
Then you posted the exact rule I was paraphrasing:
"+1 CR: Monster’s ability scores based on elite array (Do not apply this increase if you advance a monster by class levels. Monsters advanced by class levels are assumed to use the elite array.)"
Which is what I said.
"The elite array, in itself, DOES increase the CR UNLESS it's a side benefit of adding class levels."