SolidWorks should ignore the middle part options if only 2 parts are in the assembly. If it does not, you may need to hide or suppess some parts in the assembly so it only recognizes the two required parts as needing to be part of the hole series.
If you were to use a "cut extrude" in the assmbly you can RMB on the cut feature in the Feature Manager and select "Feature Scope" you can exclude components from being affected by the cut.