Erh. If you're into heavy atonement, crit>mastery for the most part (there's a specific ratio that's mathematically best between the two). Your argument doesn't really hold any relevance - "mastery wouldn't affect your damage but it would increase your atonement healing". Crit would also increase your atonement, but it has the added effect of increasing your damage.
While I'm not 100% on the exact mathematical numbers, I am 100% sure that in a scenario where you want to maximize atonement healing, crit is far ahead of mastery.
You'll also notice that the reason he asks (if you bother to read the entire three lines he posted) is because he wants to be able to use the same set for both DPS and healing - not how he'd maximie his atonement healing.