A flat bonus is usually stronger than a percentage because the Armor (and Resistance) stat is a pretty low number to begin with. I don't know exact numbers from before the patch that changed the expression from a flat value to a percentage, but "good" armor back then wasn't that much more than 100. In that case, +10 Defense would be a net increase of 10%, while the 5% bonus from a Def Mod set bonus would translate to only +5, were it expressed as a flat value instead of percentage.
Luckily it doesn't really matter, because you aren't asked to sacrifice one to the expense of another. Having a flat value for a secondary stat bonus doesn't preclude the main stat on the mod from being Defense%.
