Updates for processing of G4Commands via the G4UImanager

In ATLASSIM-3454 it was noted that many commands added to simFlags.G4Commands and then executed via the G4UImanager seem to have no effect. This was determined to be due to the fact that they were applied at the wrong point during the Geant4 initialization. In order to address this, the code has been refactored to try the commands at multiple points during the initialization until they succeed. These changes have been checked to make sure that they don't alter simulation output. They do result in more checks being switched on the Geant4 than previously so additional G4Exceptions appear in the log. Further iterations may be required.