Actually, the problem is in the description of
incorporeal touch attacks.
They aren't *actually* touch attacks. They're just so close to them and follow so many of the same mechanics that they added the "touch" part to "incorporeal attack" - as in, you don't benefit from armor, etc.
For a normal touch attack, Armor, Shield, and Natural Armor bonuses (and Enhancements to same) don't count because hitting the armor is as good as hitting the person underneath.
For an incorporeal attack, Armor, Shield, and Natural Armor bonuses (and Enhancements to same) don't count because, being incorporeal, the attackers' hands / weapons just pass through them.
However, Force effects - like Mage Armor - still affect incorporeal creatures, so an Armor bonus from Mage Armor applies against incorporeal touch attacks.
So, Ghost Touch armor acts like a Force effect as far as incorporeal attacks are concerned. It applies.
In short, yes, you're right.
