Transmutation, polymorph, wild shape, and alternate form


The Pathfinder rules are quite clear on what happens when you combine polymorph effects with size-changing effects. Namely, the size-changing effects do not function while a character is under the effects of a polymorph effect. But what about other transmutations that change a character’s physical form?

Examples: Brand, Countless Eyes, etc.

I can see this working in two ways:

  1. If a character is targeted by a transmutation effect, then a polymorph effect, the polymorph effect overrides the transmutation effect. But, if the polymorph effect is first, then the transmutation effect functions normally (by transmutation effect, I am referring to non-size-altering effects.)
  2. Both polymorph effects and transmutation effects alter the base creature, so the order in which spells are cast does not matter, as both are affecting the base creature, not the modified creature.

There is also the possibility that the transmutation effect simply does not function at all while a character is under the effects of a polymorph effect, but I have not seen evidence of that in the rules (where size-alterations are the only specifically mentioned effects that do not function).

Examples:

A druid is the target of a Greater Brand. This spell specifically states that it cannot be removed, even temporarily, unless a Mark of Justice could be removed the same way. This spell might be a specific example that says that in this case, the spell functions even under the effects of a polymorph effect. So, when the druid wild shapes, the brand would still be visible.

But, what about a regular brand spell (not greater)? Would that remain during the effects of a wild shape?

What about Countless Eyes? The druid is covered in eyes, and then wild shapes. Are they now an animal that is covered in eyes? Or does the wild shape override that effect? If they are wild shaped, and they (or someone else) casts Countless Eyes on them, does the spell function normally?

Basically, I am wondering if order of spellcasting matters.