The FCI is in effect a change to the FOM for a specific flight. (A sign of things to come). However in this regard it must count towards duty time which in this case is hardly relevant.
It may affect the weekly and monthly limits though those are hard to exceed by design.
Currently no-one can be diciplined if they arrive 61 minutes before scheduled departure. (Jeddah aside) A lawyer would laugh the company out of court if it ever went that far. I dont suspect they would even open that can of worms. Its likely to have bad implications on the whole industry as EK is not the only airline that does this.
Again the company cannot dicipline a crew who arrived 61 minutes before scheduled departure, completed all duties in a timely but safe manner and the flight departed late. Any conflict on this would result in the airline having to prove that this was normally possible - which frankly they cannot.
Its a touchy area for the industry and I doubt either party really wants to go head to head on it. The crew would be likely to win but wouldn't have a job thereafter.