there is no way EK can ever operate with only one captain and two fos for shorter trips.
If that's the case, EK don't know about it (or are ignoring it). They're selling all FC seats on Perth flights if they put an aircraft on the service that has crew rest. (Perth flights operate with one captain and two FOs.) I know of one of the senior captains who was met with this situation who told them to unsell one seat or he wasn't going. Luckily, some of the FC pax were staff upgrades, so it didn't filter up as far as I'm sure it would have if he'd have had a real FC passenger downgraded.