I don't sure if it was mentioned, but there is this funny part about certain Wondrous Architecture in Stronghold Builder's Guidebook:
Desecrated Shrine: The entire stronghold space is desecrated, as per the spell. All Charisma checks to turn undead suffer a –6 penalty. Undead in the space gain a profane +2 bonus on attack and damage rolls and saves. Undead cannot be created within nor summoned into this space. Undead summoned or created in this space gain +2 hit points per HD.
The desecrated shrine must contain an altar, shrine, or other permanent fixture dedicated to the creator's chosen higher power.
A consecrate spell negates the effect of the desecrated shrine for the duration of the consecrate spell. After that, the effects of the desecrated shrine return.
Caster Level: 3rd; Prerequisites: Craft Wondrous Item, fixture dedicated to chosen higher power, desecrate;
Market Price: 3,000 gp.

Also, similar stuff was already mentioned, but still: Powerful Build and Kobold's Slight Build
Certain transformations are remove all the SQ - including the possible Powerful Build/Slight Build
The problem? The fluff is "they're that big/small"
If the Dragonborn's Rite of Rebirth, at the very least, may be excused by "They became smaller/bigger" (weird, but OK) - then what's the excuse for Effigy, Elder Eidolon, or Ice Beast?