Found myself in Blender today, trying to get a basic UE4 Mannequin into the editor to muck around with.
Noticed the ye olde issue of Blender adding an extra bone still exists.
When I searched for a fix, I often found myself being referred back to my own ye olde page on the subject.
Hopped into the 2.78a version of the FBX exporter and fiddled around a bit, got it sorted.
Figured I share the result:
Tutorial: Prevent Blender FBX Exporter adding extra root bone](Prevent Blender FBX Exporter adding extra root bone – Kris Redbeard)
If you give it a go, please let me know if it does or does not work for you.
In UE4 Editor:
Hope someone finds it useful.