I agree with you.
If the lady has a UK work and residence permit, the passport does not matter.
However...
It may be that the company states "EU passport" for simplicity.
Writing "permanent resident and work permit" could be misunderstood by foreign applicants.
I would, in her case, write a letter to HR mentioning the fact, clearly stating the facts.
xxx
To be mentioned, however is this...
Some countries however allow EU citizens to enter without visa, i.e. Brazil.
But an American citizen would require a visa, i.e. in Brazil.
It would be the employee's responsibility to obtain such visa.
And a last minute rostering for that flight would require a crewmember with EU passport.
So that might be the only limitation.
xxx
Hope this help
Happy contrails