Old situation:
First footprint of the SOM contains outline, mounting holes, footprint of P1 and markers for positions of P2, P3 and P4.
Second, third and forth footprint contain only P2..P4 connectors.
This situation leads to a problem with the BoM, because the 4 identical connectors could not be grouped together.

New situation:
Outline, mounting holes and position markers are now located in the footprint which is assigned to the SOM placeholder
4 identical footprints assigned to the SOM's connectors P1..P4 contain only the connector footprint.
This shouldn't cause problems with the BoM.