Damage Reduction is not a penalty. Penalties are negative bonuses applied to a roll, e.g. for having low Strength.
As such, your quote has nothing to do with the situation where you deal one-or-more damage, but the enemy has DR in excess of that damage (and you don’t overcome it). In that case, you do not deal any damage at all, nonlethal or otherwise. This is true for anyone, undead or living.
From the PFSRD:
Some magic creatures have the supernatural ability to instantly heal damage from weapons or ignore blows altogether as though they were invulnerable.
Whenever damage reduction completely negates the damage from an attack, it also negates most special effects that accompany the attack, such as injury poison, a monk's stunning, and injury-based disease. Damage Reduction does not negate touch attacks, energy damage dealt along with an attack, or energy drains. Nor does it affect poisons or diseases delivered by inhalation, ingestion, or contact.