Does your workflow work properly for projects without Skybox?
If you're in a hurry, I would suggest rendering an intermediate file format out of AE (like QuickTime with the PNG codec) and then bring that file into the Adobe Media Encoder. In fact, if I were you, I would open it in AE CC 2014 to render with multiprocessing enabled (assuming your machine and project can work with multiprocessing).
Same goes for me, maximum render resolution allowed by the mov format (h.264 codec) in compositions with mettle skybox is 2000x1920 px.
No option for .mp4 file format either.
Is that a native limit? Any possible implementation?