I finally managed to find a work-around to creating a 48fps sequence, which was to drag-and-drop the 48fps clip onto the "New sequence" button. My problem now is that Adobe's Media Encoder (File -> Export -> Media...) doesn't have a frame rate option for 48fps. Does anyone know if there's a way to enter custom frame rates?
Not exactly a direct answer for Media Encoder, but you could bring your sequence into AE and export from there? I've only tried with Animation codec, but i've successfully done non standard frame rates out of AE.