the MER tool does add bubbles e.g. when pressing the space bar. It only reacts when you’re in the main window (i.e. click on the main window first, then move around the trajectories and press space).
You need to activate keyboard control for one of the trajectories in the MER viewer, first, however.
This being said, I think it’d be much easier for you to plot the points manually (e.g. using plot3() function). The Lead-DBS Viewer is nothing but a Matlab figure, so you can add anything you want to it using the normal Matlab commands.
Finally, the coordinates in the figure you sent were plotted with lead group (use color points by regressor, set the regressor to all ones and instead of plotting electrode trajectories, plot point clouds).
Hope this helps!