The only Rift RB that I know of that levels crystals is the one in Hero rift. He levels crystals from 12 to 13 at a 8% chance (when it succeeds, all crystals in the party levels up).
It has been a rumor for a very long time that the commander rift boss (the one in the lvl 70-80 rift) can level soul crystals 10->11 and 11->12. But there never, ever has been any kind of real confirmation of that. No screenie, no fraps, nothing. Only "I know a friend who knows somebody who says his clannie did it" kind of reports.
The hero rift boss can level 12->13 (and only that), and that is confirmed and people are doing it all the time.
I am not sure if it was only a rumor. An unmentionable site (that gathers drops) had him in the list of mobs that level the a.m. crystals (before Interlude) but not any more. I imagined that since it was based on actual data, it would be true.