
Aunasiel |

I originally thought the same until I reread the section in the Core that covers staves.
From Page 491:
"Staves use the wielder’s ability score and relevant feats to set the DC for saves against their spells. Unlike with other sorts of magic items, the wielder can use his caster level when activating the power of a staff if it’s higher than the caster level of the staff."
I may be over analyzing it, but it looks like it changes Save DCs and bumps up caster level to the wielder's level if above CL of the staff.

Jeraa |

Continue reading. It is not just for spell DCs, but all purposes.
This means that staves are far more potent in the hands of a powerful spellcaster. Because they use the wielder's ability score to set the save DC for the spell, spells from a staff are often harder to resist than those from other magic items, which use the minimum ability score required to cast the spell. Not only are aspects of the spell dependent on caster level (range, duration, and so on) potentially higher, but spells from a staff are also harder to dispel and have a better chance of overcoming a target's spell resistance.
Overcoming spell resistance is a caster level check. Spell Penetration improves the characters caster level for the purpose of overcoming spell resistance. Therefore, that improved caster level is used if it is better then the staffs.
Staves use the wielders numbers if they are better than the staffs. IT doesn't matter how the wielder got those scores, as long as they are better than the staff itself.