"The FAA rule change was completely arbitrary and unfounded. We had been doing it that way for decades with no problems

Unfounded? You have one pilot qualified, and one not (technically) on the flight deck.
I brought this up on my OE. They said the same thing. "We've been doing this for years".

OK. Then maybe you've been doing it WRONG for years.
I saw this A LOT while working for the FAA while I was furloughed. Signing off things that weren't legal... but that's how they (the office, or CMO...) have been doing it for years.