I am familiar with the differences. I just do my validation differently. Yes, a multiuser environment can be a hastle. As for a toolbox appearing in any new project, ...at least at the single user level, ... is readily handled under Project, Options, General, Default toolbox (use the same toolbox as the default for all projects). BUT that won't help if you have several toolboxes to use.
Good luck... maybe put in an ArcGIS Idea if we haven't overlooked something simple