Putting some or all 787 under Fly Dubai hampers one of its greatest assets for EK: MFF with the 777 family. This is a huge advantage in terms of daily flexibility (and at the same time hints against a 350 fleet).
As long as there are many EK routes prone to such flexibel deployment for different sized aircraft, i guess the 787 will be flown under EK flag.
On top of that, there is no MFF (at the moment) between 787 and 737.
There might however be some FZ routes permitting 787s, but those routes might be changed to EK before FZ would get a small numbered additional fleet.
This might sound bad for FZ pilots. I have always advocated for a start at FZ for cadets and new skippers in Dubai, with a swap to EK after a few years. This would take out jealousy and politics in pilot-staffing, would increase experience in this region and therefore overall airmanship in the group, plus it would be the more flexibel and therefore cheaper solution.