If you choose Martial Versatility with Weapon Focus, does it count as you have Weapon Focus with the rest of the weapons in the group for purposes of applying Penetrating Strike or is it just the bonus of Weapon Focus that applies and not "having" the feat?
Martial Versatility (Combat, Human) - "Benefit: Choose one combat feat you know that applies to a specific weapon (e.g., Weapon Focus). You can use that feat with any weapon within the same weapon group."
Penetrating Strike - "Benefit: Your attacks with weapons selected with Weapon Focus ignore up to 5 points of damage reduction. This feat does not apply to damage reduction without a type (such as DR 10/—)."
I'm going to say no. MV says you can "use that feat" so you're using Weapon Focus (rapier) when attacking with a short sword.
PS says weapons selected with Weapon Focus. You haven't selected short sword with weapon focus, you've selected rapier. Even though you can use weapon focus (rapier) with a short sword.
If PS said "Your attacks benefiting from weapon focus..." or something similar, then it would work.
I don't think that it would break anything to be run otherwise, though.