All settings regarding presets transitions are under visualisations/configure plug-in/transitions
Other than that, it should be possible to send messages to milkdrop using some sort of script but I don't know how. I remember AidenRigel's milkdrop interface which certainly had this option, but he and his site www.lightmaestro.com
seem to have disappeared from the planet.
The third option of course is to control preset changes manually