If you specify a "property" key in the executable action descriptor (the one you give to executeAction, not the descriptor for the metadata settings) , it should just get/set generatorSettings->property.  So you could specify the plugin name as property to scope the access to a particular plugin's settings. Something like this (not tested, but I think it gives you the general idea):

        var classDocument = charIDToTypeID('Dcmn');
        var propGeneratorSettings = stringIDToTypeID("generatorSettings");
        var propBla = stringIDToTypeID("bla");

       var theRef = new ActionReference();
       //NOTE: property needs to be defined first in ref or it won't work.
        theRef.putProperty(classProperty, propGeneratorSettings);
        theRef.putEnumerated(classDocument, typeOrdinal, enumTarget);
 
        var pluginSpecificDescriptor = new ActionDescriptor();
        pluginSpecificDescriptor.putBoolean(propBla,true); //whatever your plugin settings need to be.

        var setDescriptor = new ActionDescriptor();
        setDescriptor.putReference(propNull,theRef);
        setDescriptor.putObject(keyTo,classNull,desc);

     /// put pluginSpecificDescriptor into "myAwesomePluginName" key within generator settings.

       setDescriptor.putString( stringIDToTypeID( "property" ),"myAwesomePluginName"); 

        executeAction( actionSet, setDescriptor, DialogModes.NO );