I know what you're saying. What I'm saying is that rapiers used to bypass ALL protection offered by vanilla armour. I've been lead to believe that they now only bypass a portion of that protection (e.g. diamond armour gives 80% damage resistance. Does the rapier ignore all 80% of this damage resistance, or only a portion of it (so it only offers say 60% resistance))?It answers your question perfectly, IF you know what armour is classed as what
Let's make it easier...
If the mobs are only wearing vanilla armour a rapier that has the same damage output as a cutlass (for example) will do more damage to the mob, as it bypasses the armour. However, some modded armour can be this special armour, although, I can't recall any special armour worn by mobs, and if it is worn, then both swords would be just as effective, however your "bonus" probably makes the other sword (not the rapier) better. As the rapier's bonus is that it bypasses armour, while other swords do other things, e.g. the cleaver increases the chance that a mob drops a head when killed.
I'm fairly sure this is now the case, since I case across a gold armoured zombie a minute ago and the rapier left it with half a heart, rather than killing it outright as it used to. I'm not sure though, it could have been a special zombie with extra health.