When you state that you "have the Kuka with a spindle at the 6th axis" - what does this actually mean. I see two ways to do it, I expect only the 2nd option described below will results correct output:
The spindle is defines in the robot assembly. No special changes in MTB.
The robot includes only the robot (up to J6), while the spindle is defined as a head in MTB with a mount and tool junctions. Mount JCT should be where the spindle is mounted to the robot while the tool JCT is where the tool is mounted to the spindle. This also requires the spindle to be added as a head by the operation.