The Trent 900 will fit into a 747 freighter, it was a prime design criteria. It is a tight fit using a special stand that "rolls" the engine on it's side so the engine can drop down lower in the stand.
However this does not apply to the Engine Alliance GP 700 series Emirates use on their A380s. The engine has to be shipped as a separate core, separate fan case and a set of fan blades, plus all the tooling to build up the engine at a remote site. The only other option is to charter an AN124 or similar outsize cargo aircraft to allow the engine to be shipped complete.
Same applies to the GE90 engine on 777-200LR and -300ER.