I've only done DRK and SAM, so those two are the only ones I can comment on.
DRK
It's implied that Blackest Night is invoked using memories of Haurchefant and/or Ysayle, based on Myste's last line before disappearing and some other context in the quest line.
SAM
The technique you learn from the 70 quest, Guren, is probably an imitation of a technique you see Ugetsu using during the Battle at Bekko. Since you both trained under Musosai, it would make sense you'd be able to use the same ability.
As for the AF gear and weapon... whoooo knows...? You just kind of get the chest with the items from nowhere, so I'm not gonna think about it too hard. (Still hoping they eventually let me upgrade and dye it. I might switch back to maining DRK if they do.)