I would guess it's a flutter problem. Flutter is when an aircraft becomes dynamically unstable due to the interaction between the aircraft structure and the air around it. Certain aircraft are more prone to flutter than others such that it occurs at speeds closer to its max airspeed. The type of engine and how it's attached to the wing can have a big effect on flutter since it's a large mass that's hanging off the wing. As a result the same aircraft with different engines can have significantly different flutter properties.
The restriction is to 747-400 vs 747-400ER models. The former are powered by RR engines (at least, at Quantas) while the latter are powered by PW engines. The 747-400ER has not been certified with a fifth engine pod.
Qantas flies one 747-400 with GE, though. (and 4 with RR) I was thinking there might be a contractual issue with GE over this, like GE will just swap the engine on demand at their own expense at any station.
Duly noted. That one /is/ an odd one, though -- it's a 747-48E that was originally from Asiana, so it might not even have the mount for the 5th engine (as it's an optional extra). Still, you are right that it makes more sense to be related to contracts with the engine mft.
Why the restriction to RR-powered 747s?