Transmutation, polymorph, wild shape, and alternate form

Question

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? A normal animal would not have such a brand. Does Wild Shape allow the druid to become an animal that is unbranded?

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? A normal animal would not be covered in eyes (there are no animals I know of with all-around vision). Would the Wild Shape effect override this ability?

Basically, I am wondering if order of spellcasting matters.

There are two sections of rules that also come into play in this regard, potentially in contradictory ways:

Combining Magic Effects

Spells or magical effects usually work as described, no matter how many other spells or magical effects happen to be operating in the same area or on the same recipient. Except in special cases, a spell does not affect the way another spell operates. Whenever a spell has a specific effect on other spells, the spell description explains that effect.

and

One Effect Makes Another Irrelevant

Sometimes, one spell can render a later spell irrelevant. Both spells are still active, but one has rendered the other useless in some fashion.

The second section seems to imply #1 while the first section seems to imply #2. And in this case, both of these sections of rules seem to apply equally depending on how one interprets the phrase "original form".

Edit: The answer below implies that interpretation #1 is the correct interpretation. However, that did not settle the discussion with my group. The main argument for option #2 is as follows:

If you generate a polymorph effect while under the effects of a form-altering transmutation effect, then the form you change into is a polymorphed version of a creature under the same transmutation effect. The "normal form" that you change into is whatever the normal creature being effected by the transmutation effect would be under the effect of said transmutation. This coincides with the general rule for Combining Magic Effects listed above. In other words, if the new creature could be affected by the spell, then its "normal form" would be affected by an already active spell.

I am not saying this is the correct answer. I am just saying it is the best argument I've heard for why option #2 may be the correct answer. I am still torn between the two.

Answer 1

Relevant quote from the original sourcebook:

While under the effects of a polymorph spell, you lose all extraordinary and supernatural abilities that depend on your original form (such as keen senses, scent, and darkvision), as well as any natural attacks and movement types possessed by your original form. You also lose any class features that depend upon form, but those that allow you to add features (such as sorcerers that can grow claws) still function. While most of these should be obvious, the GM is the final arbiter of what abilities depend on form and are lost when a new form is assumed. Your new form might restore a number of these abilities if they are possessed by the new form.

This seems to indicate that such form-based effects would be suppressed while the polymorph is active, but as suppressed spells still have their duration expire, the duration would continue to go down. Of course, as the cited section indicates, the GM can determine that the spell affect still applies to the new form, and gives all benefits and drawbacks. In the former case, the following point from the Stacking Effects section applies:

One Effect Makes Another Irrelevant: Sometimes, one spell can render a later spell irrelevant. Both spells are still active, but one has rendered the other useless in some fashion.

Likewise, there is nothing to indicate that transmutation spells would not affect a polymorphed creature, so they would function normally.

Edit: The OP has given an argument that 'original' in this case refers to their true form, and as such, transmutation effects would not hold with a polymorph. In the rules, 'original' form is clearly meant as a contrast to the polymorphed form. Otherwise, a creature that used a ritual to gain an extra pair of arms would keep them no matter what form they turned into (imagine turning into a dragon, and having a tiny pair of human arms stuck to your sides!), and a reincarnated creature would only lose abilities from their original race, not the new one!

Although, reading over everything a second time, there's actually a better argument for why those changes would stay. The cited rules state "...you lose all extraordinary and supernatural abilities...as well as any natural attacks and movement types...You also lose any class features that depend on form...". A transmutation spell doesn't fall under any of those categories (since a spell or spell like ability is not extraordinary or supernatural, but a permanent addition of arms would be extraordinary), and as such, would not be affected.