Royal Authority turning into Atonement would probably be fine. At least, I can't think of a scenario where you would want to do Royal Authority with Sword Oath stacks remaining.

Requiescat turning into Confiteor, on the other hand, has some issues. Namely, if you are mashing Requiescat late into your GCD (like during a double weave), then you may end up queuing Confiteor, immediately ending Requiescat.