The line only applies when one side of the polymorph any object is an object
Polymorph any object allows you to turn an object into a creature, granting it 5 Intelligence if it had none before, or a creature into an object.
This spell functions like greater polymorph, except that it changes one object or creature into another. You can use this spell to transform all manner of objects and creatures into new forms—you aren't limited to transforming a living creature into another living form. The duration of the spell depends on how radical a change is made from the original state to its transmuted state. The duration is determined by using the following guidelines.
It may initially seem ambiguous if you could alter between a creature or object; luckily, this is exemplified in the table by turning a humanoid into a marionette or a sheep into a wool coat.
- (4) (3 hours) (Human to marionette)
- (6) (2 days) (Sheep to wool coat)
Because all interactions with objects do not qualify for greater polymorph (they only work because of the exception in polymorph any object) the list of spells (beast shape et al) are not applied and modifications to Intelligence happen.
In a sense, the modifier is a duration bonus for turning a creature into an object that does not exist when turning an object into a creature.
Ignoring the portion of polymorph any object that allows you to "duplicate the effects of" other spells, and only applying it's default mechanics, here are some use-cases: (pao = polymorph any object, gp = greater polymorph)
- Human into Wolf
- pao functions as gp functions as beast shape IV; no Intelligence change, +2 modifier
- Wolf into Human
- pao functions as gp functions as alter self; no Intelligence change, +2 modifier
- wolf into wolf statue
- pao acts on itself; intelligence becomes 0, +2 modifier
- wolf statue into Wolf
- pao acts on itself; intelligence becomes 5, no modifier
Side note, I don't believe baleful polymorph cast via polymorph any object has its duration altered. Keep an eye on this related question for more information. My belief is based on this current answer and my own interpretation.