These basically set weaknesses.
If an enemy weakness is set to fire, and a projectile type is set to fire, then that enemy will take twice the damage it would if the projectile was set to something else. Of course, if your enemy has 1 HP, then it won't make a difference. But if it had 4 HP, and you had those settings, then it'd only take 2 shots to take out the enemy instead of 4.