The seer does not detect a player's role, merely their alignment. There are two exceptions: puppets and familiars, which are directly detected by role. (Not sure why the familiar is not detected as a member of the vampire faction).
The question How to determine which item/role mechanic overrules another, if they contradict each other? answers what the sequence of applying auras and effects is. Before the Seer's check completes, each of these effects is applied over top of eachother. Some of these effects can change a player's alignment and/or perceived alignment.
Another related question is Bloodhound(-type) result on Damned. From this answer we can infer that the Seer will be able to detect the Damned effect, but only if no effect rated above 70 changes alignment. Looking at each of these effects:
71 Abysmal Armor should not change the result: the Seer ability does not have any text indicating that a Role-Block will stop them from identifying their target. Of course, if the Seer is wearing it, they can't use their ability.
72 Pollymorph potion should not change the result. Even when transformed, Parrots can still be evil werewolves or vampires at heart, belying their innocent appearance.
85 Resilience, and
88 Weakness both have to do with Role-Block. As per item 71, this should not affect the seer.
99 Shadow from 'Veil of Shadows' will override the Damned effect, making the player appear as an innocent villager.
100 MartyrsProtection is, I assume, the Messiah. This does not change the faction of the Messiah (merely makes this person impossible to kill) while they still have it, a damned Messiah is still damned, so should not affect the seer.
The reality is a bit more complicated with this one however: After resurrection, a Messiah can lose some of the modifiers conferred to them by other players and items. This can affect things indirectly via numbers 71-99. For example, a Damned Messiah wearing a Veil of Shadows can, when killed by a Werewolf get his Veil of Shadows stolen, and appear as follows:
- As a 'Villager' before being killed (the day before the murder).
- As 'Damned' on the day of the murder.
- As a 'Villager' when they resurrect. (Although unnecessary to do so, the Messiah reveals their role and thus their true alignment by resurrecting).
But, in the case where the Messiah takes their own life (and can thus keep their Veil), he would still appear as "Villager" on the day of their murder. This reveals whether the Messiah was the target of a werewolf or vampire.
PrimedBearTrap, StrengthOfFenrir, SpittingFeathers, and PaxDemocracia I have no idea what these are about: Either the items are undocumented on the official site (the first 3) or I don't know what the effect name would be referring to (ambiguous) for the last one.
The other unmentioned effects from 71-999 do not alter a player's role or faction in any way and should have no effect if present on the result of the Seer's ability.