What GUI applications are available to customize the Xfce 4.10.1 menu system at this point in time?
The problem still appears after all these years that it is something that the developers of Xfce must do themselves. The reason being that they know the code, and that they could easilly adapt that code for use in a simple little app that:
1. Backs up the default arrangement at any one point in time.
2. Displays a GUI of the menu and allows drag and drop of items.
3. Perhaps one part would allow hiding those menu categories not needed, and creating new ones that are.
One of the funny parts of the whole problem is that installing any application may actually create a new category and application item. It could be a Gnome or KDE app, or even something else. If this is done by programs and installation routines outside of Xfce, then there already is some sort of interface available to all. Go figure.
I don't agree it has to be the developers. I would think any programmer could write such an application. The easiest way may well be to take one of the existing ones like alacarte and just fix what doesn't work. Whether this can be done without breaking it on other desktops would be the only issue.
The other issue you mention would probably be a distro issue. It is caused by the desktop file that is created by the packager of the application.