For the optical physics messenger, there are apparently duplicate commands. Some don't work. For example, /process/optical/defaults/scintillation/setByParticleType true # works /process/optical/scintillation/setByParticleType true # doesn't work (as far as I can tell) As noted in bug 2020, documentation is incomplete.
Fixed. Note that commands with 'defaults' in the command string are deprecated and will be removed in the next Geant4 major release. Instead, use the same command without the 'defaults'.