Can palparked Pokemon change their ability after transfering?
Probably not, and therefore some can have ability nr.2 but actually have the first, which was the only available in 3rd generation.
I was pretty sure about this, until I wanted to create a clefable and looked it up on http://www.smogon.com/dp/pokemon/clefable
Every build there has the ability Magic Guard, but still 3rd generation tutor moves, like Softboiled or Seismic Toss...
Are those illegal sets?
No they aren't illegal.
A Cleffa/Clefairy/Clefable will always have Cute Charm in 3rd generation, and it will stay Cute Charm when Pal Parked. However, when the Pal Parked pokemon evolves in 4th generation, if its PID would make it Ability 2, it will change to Magic Guard.
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