I think the real problem is that Impervious bypasses the Toughness save system instead of working with it. A better solution would be to have Impervious + [some number] be the minimum amount by which the bearer passes any Toughness save even if their roll would normally make it worse. Now it's no longer a game of "+1 Tag". Penetrating would then lower the minimum save, making it so that a few low ranks don't completely negate the power but also encouraging high ranks to get in full hits.
If we set it at "15 + Impervious" that means the character will automatically pass any save of +10 or less, equivalent to Impervious 10 under the 2e system. But now +11-+14 results in, at worst, a Bruise, +15-+20 at worst Stunned+Bruised, etc.
"15 + (Impervious/2)" makes it equal to the 3e system. Up to +5 bonus: invincible. +5-+10: max One Degree.
Of course this may make Impervious too good in that it "locks in" a minimum die roll. I did just come up with the idea after a couple seconds thought and I'm no numbers genius. Still, as I said in the quote above, it does eliminate the "+1, now it's useless" problem. Also it kind of makes more sense to me this way.
I'm hoping someone can tell me a way to make this viable without making it too complicated.