Would Maximize (or Empower, or any other variable affecting metamagic) affect the damage of new attacks granted by polymorph spells? Could I use a Greater Maximize Spell metamagic rod on Form of the Dragon III to always deal 96 damage with the breath attack?
What he means is that the Metamagic feats specifically function on the "random, numeric" effects of the spell.. like xd6 damage froma fireball for Empower Spell or Maximize Spell.
Form of the Dragaon, and other polymorph spells, generally do not have random numeric effects. Empower and Maximize do not enhance the "secondary effects" of the powers that come with the form you change into (although Extend would let you stay changed longer).
I think more specifically, the ´effect´ of the spell is the spell´s effect on it´s TARGET(s).
In cases of using Polymorph spells on yourself, you yourself are the target, and effects targetting you could be affected by these MM effects. So if there is a Polymorph spell granting you the ´Fireball Booger Shooting´ ability (Fireball at-will for duration), the Fireball Boogers will not be affected by Maximize, et al. If you gain a CON bonus from a Polymorph spell, you should get max HPs if you Maximize the spell.
This isn`t that different than if you Summoned some creatures: Maximizing that spell might affect the number of creatures, but it`s not going to apply to effects of other things they might do, like using a Breath Weapon.
The Breath Weapon wouldn`t be maximized any more than the Natural Attacks would be.