The current ruling, of course, defies the logic of the rules which state that a creature moving from one size category to another gains certain benefits and disadvantages as described in the MM.
In short, the designers of the PrC probably never thought about the consequences of a PC undergoing a permanent size-change, so the Sage had to cover their butts by issuing a ruling that is one more exception to the general rule.
Why do I feel like D&D 3e is becoming like Chemistry class? First they tell you, "Here are the rules and they are fixed" and then proceed to describe all the exceptions to those rules. I have a similiar problem with the Enlarge and Reduce spells. Both can potentially change your size category but you gain none of the benefits and suffer none of the drawbacks of that change.