well... most of phys abilities scale from more then one source. even hunter and scoundrel increase your damage.
you just need to imagine a proper explanation to get rid of the confusion.
like Hunter courses labeled "high ground will make you win, here is how: *showing StarWars ep.3*
or Scoundrel: "check all the pictures with a "back" amond them"
or warfare guide for necromancers: "armor looks like this, avoid it at all costs when casting"
most of the confusion (as I see it) comes from the fact that there is only 1-3 fire\water\etc. sources (wand, grenade and spell), while simultaneously there are 7-8 physical weapons (bow, spear, dagger, 1h, 2h, staff, spell, grenade)
