The way I built a LibreOffice SFS using PaDS (referred to in my prior post) was after the SFS was created I mounted it, copied its contents to a NAMED folder, then dir2sfs the folder. But before running dir2SFS I edited the desktop files in /opt/libreofficeX.X/share/xdg to remove the %U arguments from Exec=.
LibreOffice symlinks those desktop files to /usr/share/applications. Those symlinks create the menu entries.
Since I mostly use writer and calc, rarely impress and draw I don't bother editing the other desktop files.
I think what you can do, having already built the SFS, is make the changes in /opt/libreofficeX.X/share/xdg, execute a Save --which will preserve those changes to /opt-- unload the Libreoffice.SFS, edit the problem lines in jwm.rc in text editor, then reload. Other than editing the files in xdg, I'm not certain if all those steps are necessary because my build as above described does not have the %U arguments in the jwm.rc file. The changes in the /opt folder in your SaveFile/Folder should have priority over the code of the SFS.