I haven’t added this setting to be user controllable in Board2Pdf. It sets the Drill Marks to Actual Size for copper layers, and to None for any other layer.
if pcbnew.IsCopperLayer(layer_info.id):
plot_options.SetDrillMarksType(pcbnew.DRILL_MARKS_FULL_DRILL_SHAPE)
else:
plot_options.SetDrillMarksType(pcbnew.DRILL_MARKS_NO_DRILL_SHAPE)
Can you try the File → Plot dialog in KiCad to see if you can get the result you’re looking for? If so you could add a feature request to Board2Pdf.