Well the latest TSB I have is #01-15-7 it is a tsb that states do not mix mercon 5 with any other type fluid . That includes mercon 3 or mercon.
The reason is that the seals can start to swell and leak and also cause driveability and longevity issues with the tranny.
I would get it in writing that they made a mistake and will repair the tranny in the future if you have issues later on .
This is of course that they don't have a later tsb to back the service guys statement.
Just my $.02
Rich