Thanks again for your comment.
In Unity, there are some ways to change the pivot using script, which I don't really want to do.
I want my models to be ready-to-go straight out of Qubicle for ease of use.
To be complete, here are the (un-tried) links I found:
To wrap this up for now, untill Qubicle adds some support for parenting I just export two loose matrices into one fbx and create my hierachy to create a Prefab in Unity. For now, the hiearchy seems to remain intact when I just add some voxels or colors and re-export, which is what I wanted to be able to do
As for the pivots, my workaround 'solution' is to create models/matrices that are symmetrical, so that the pivot can always be in the center. It indeed means my helicopter rotor is now twice as thick .
Diederik / Xform
LAST MINUTE NOTE: I just saw that the example Deer has it's pivot neatly set to half voxel, so it is indeed possible. But I saw that the model position cannot be set to halfs, so that after exporting the pivot is correct but the position is not 0,0,0...