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Advanced doesn't tell you whether or not it is inherited or acquired.
I've always though of it as inherited. You have an advanced T-Rex. Not a normal T-Rex with an advanced - skeleton template.
In this case the Wis/Cha advancement of the Advanced template is ignored when the acquired template of skeleton is applied.
Ultimately it is up to the GM. I will point out that I just did a DB search of all monster published by Paizo. There is no example of an advanced skeleton creature.
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