Hi C -
I am going to run a specific test again regarding the launching of a project with Substance plug-in but you should starting with 4.7 be able to place the plug-in into the launcher version which includes the full source code and launching should package the project with teh correct plugin settings.
Take a look at this wiki entry I did for another user a while back about installing the Substance plug-in, you can check it against your steps.
Thank You
Eric Ketchum