I've got an "Irradiated Plasma Thrower" that I modded into a flamethrower. I think the damages are like 100 each for Ballistic, Energy and Rads. It drops Super Mutants all the way up to Overlords like they were cardboard targets.
So, even though "most Wasteland critters" are supposed to be immune to rads, if not buffed by them, I have to question if it is working as intended on that. I think it is possible that, rads from the environment: yes they are immune, and it is possible that a weapon that does "only" rad damage they might shrug off.
But I wouldn't be surprised if a weapon that adds rad damage to other types is being miscalculated and the critters that shouldn't be hurt by the rad quantum are in fact being hurt by that portion.
Re: super Mutants, I am not sure how their damage resistances are treated. My guess is that all Super Mutants have built in damage resistances, and that these increase with the "level" or tier of the mob in question. So an Overlord probably has a lot more than a Butcher, who has more than a standard version. Whether ANY of the Resistance in any of these cases is treated as "armor" I would have to question, and my guess would be "no, unless the critter in question is ALSO wearing a set of lootable armor" (which seems very unusual, and if memory serves, only happens with a few boss mobs . . . in fact, I'm not sure I've found Super Mutant armor in any way except just laying around in their lair or in a container). So, my guess is that "Penetrator" is really only effective against humans (who are wearing armor), coursers, some synths (the ones that have armor in their inventories), and a very small set of super mutants.