Pretty sure they are different in that way. Rafas "Truth" skill is treated like normal magic. Higher her faith, more dmg; Higher her targets Faith, also more damage. However Malaks Untruth is the opposite, and in fact if you click on his portrait, he says something like "Untruth hurts those with low Faith. Believe, or you'll pay"- something to that effect. Untruth hits harder on lower faith targets I believe

However, I think what someone was referring to is a bug in that when you cast Faith on a target, Untruth hits them harder than it should (and reversely, casting Innocent makes Untruth do 0 dmg unlike the description says it should do)? I dunno, I haven't used Malak to know if thats true