The only way to skip nodes when generating data is to enable 'Only selected nodes' option. Obviously this will not scale when the model is large. However, the most recent binaries (you know the link already) will pick the selection from the main graphical view. This feature, combined with DIagnosis|Select Nodes command in the main menu makes the task easy. Select targets first, then don't forget to keep Shift pressed when selecting observations.
Alternatively, color your observation/target nodes using the same RGB (Diagnosis|Autoformat) and select nodes by color from the Edit menu.