Refused screen repair due to third party battery

Yesterday I took my iPhone 6 in for a screen repair. When I checked-in I informed the employee that my phone had a third party battery, they said it was fine and even made a note on the details:

"Issue: accidental physical damage - device has been presented with multiple cracks to the display as a result of accidental damage. customer has declared that no other known issues are present with the device.

Steps to Reproduce: All issues reported by customer have been validated and are present.

Cosmetic Condition: Internal battery is third party. Proceed with display repair."

To my surprise when I went to collect it 1.5 hrs later they told me they hadn't completed the repair because they can't touch iPhones with a third party battery.

Has anyone else experienced this? If this is their policy then that's fair enough but why was I told this was an issue when I checked-in? The staff at the Reading store had no apology for the fact that I'd wasted over an hour waiting only to be told this.