Only way i could find to do this was to revert to javascript via the do javaScript
command
Seems the javascript mode in PhotoShop has some lower level hooks that can solve this particular problem.
e.g,
set js_code to "function SelectTransparency(){
var idChnl = charIDToTypeID('Chnl');
var actionSelect = new ActionReference();
actionSelect.putProperty(idChnl, charIDToTypeID('fsel'));
var actionTransparent = new ActionReference();
actionTransparent.putEnumerated(idChnl, idChnl, charIDToTypeID('Trsp'));
var actionDesc = new ActionDescriptor();
actionDesc.putReference( charIDToTypeID('null'), actionSelect);
actionDesc.putReference( charIDToTypeID('T '), actionTransparent);
executeAction(charIDToTypeID('setd'), actionDesc, DialogModes.NO);
}
SelectTransparency();
"
tell application id "com.adobe.photoshop"
activate
do javascript js_code
end tell