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Plague doctors wore the masks because they put PERFUMES and herbs in the beak to counteract the putrid air of disease.
It was a common belief at the time that disease was caused by foul-smelling air itself, with no idea about airborne viruses or bacteria.
Plague doctors were hired by towns to help the sick during epidemics. Due to their primitive ideology and methods MOST PATIENTS DIED. Additionally, most plague doctors weren't qualified well and a majority of doctor's themselves died.
As time went on, plague doctors changed from being helpful to being a sign of death. More often than not the sight of a plague doctor meant someone, a friend, family, or neighbor, is dying and would be quarantined.
You can see how, being close to death all the time, plague doctors had a bad rep.
>Perfume Pokemon
>Bird Pokemon - No flying type
>Fairy-type (indicative of the time period)
>Exclusive to the version with the death motif
>Healer ability
>Beak that resembles mask
All the traits are there; whether the Pokemon WILL OR WILL NOT follow this path still remains to be seen; however, it doesn't seem too far out of the range of speculation for it to change as it evolves.