Copied from the Gitub issue to continue the discussion here:
I found a solution! 
Tested with a very simple single jointed example.
It seems the GLTF2Loader does support transformed pivots. So the process goes like this:
- Install the blender gltf2 exporter
- Export the file as FBX from your preferred software.
- Load the FBX file in blender (needs to be binary format 2015 or earlier)
- Export as GLTF2 ( I used .glb binary format)
- import in three.js and the results for this simple example look like this, and the animations play correctly (with a bit of tweaking of exporter settings)
For reference the same file imported with the FBXLoader looked like this (see the github issue for full details)
I’ll be testing with more complex examples over the next couple of days, I’ll report progress here.