Is it intentional that (some?) the War Plans "activity trees" only apply when it's an active objective in the War Plan?

Had just grabbed the "spawn a Horadric Altar after 30 elites" node in the Nightmare Dungeon tree, ended at 28 in my last War Plan dungeon. Figured I'd run one more to kill two elites really quick, but the counter didn't go up at all. Not sure if it's bugged or if the perks only activate during a War Plan activity, which is kind of a bummer if so. Anyone know if there are other perks that only work during War Plans, or if they're all meant to be that way?