No it's not possible, but I know it's often useful, so I have been thinking about some plugin that works around it.
My suggestion for now, not so elegant perhaps, but works, is to drop one structure onto the other in the Builder, then the new atoms will be added (and selected) and you can e.g. turn them to ghosts or make them more transparent.
This, however, will not work nicely if also the cell dimensions are different...
