Super penetrator does one thing and one thing only...it prevents a shot that penetrates the hull from stopping at the first module it intersects with.
It does not change penetration chance. If you penetrate, a rail gun will do almost no damage to the hull, because the breach damage is such a large fraction of full damage.
It does not, I believe, change maximum penetration depth. If you couldn't reach the module from a certain angle before, and not due to interposing modules, but sheer depth, you won't reach it with super penetrator either.
What it does do is allow a module to be hit irrespective of those interposing modules and damage all modules in a line up to maximum penetration depth. For example, if you are directly behind a corvette and target it's FSD a normal rail gun will hit the power plant, and only the power plant, because it's in the way. With a superpen rail, you hit both and do full damage to both (and possibly other modules).