【解决办法】本地验证设置可以生效,需要保存地图和工作空间:
Map map = new Map(workspace);
String mapInfo = workspace.getMaps().getMapXML("map111");
map.fromXML(mapInfo);
Layer layer = map.getLayers().get(0);
ThemeGridRange theme = (ThemeGridRange) layer.getTheme();
theme.setSpecialValueTransparent(true);
map.refresh();
workspace.getMaps().setMapXML("map111", map.toXML());
workspace.save();