The different thicknesses among the offered head gaskets help compensate for a manufacturing tolerance in piston protrusion. If I were to suggest a single head gasket thickness, it would be the thickest gasket. This would accommodate a worst-case piston protrusion scenario, while producing only a slightly lower compression ratio for those engines with minimum protrusion.
The early Duramax 6600 was produced with an 18:1 CR and the latest Duramax 6600 is currently running a 16.8:1 CR. The slightly lower CR that a .004 thicker gasket might produce would not noticeably affect the Duramax.