I think it does actually.
I played one with no 9% mastery and my mana regen at lv 12 was 40. I played another game where the only thing I changed (including what items I had at level 12) was adding the 9% mastery and my mana regen at level 12 was 53.
53 is a lot more than 43.6.
Without the 9% mastery my mana regen was 53 at level 18.
With the 9% mastery it was 53 at level 12.
I didn't make it to level 18 on my 2nd game, so I dunno what it was at lv 18 with the mastery, so I'm gonna have to do more games till I can get that number, but as of now I think the mastery applies to the ambient crystal scar regen buff. ;oD