Hi Ted,
We'll take a look at revising the text to make it more clear in the next release, as the double negative at the beginning is a bit confusing.
Using Launch Arcmap by default: When you make changes and save and close the step the mxd used for that session is saved with the job. This allows users to perform some of their work and return to the same mxd upon Launching Arcmap over and over again, when they come back the next day for example. This mxd can be deleted when the job is archived or deleted or as part of the CleanUp custom step as an option.
If you use the /nosavemxd, every time Launch Arcmap is executed for that job it will load the template map stored for the job type. It will preserve none of the configuration performed by the user.
JTX_MAP_STORE shows all the maps that have been added via the Administrator toolbar in Arcmap or through the Workflow Manager Administrator for use as template maps for Job Types. Or, they can also be used as the display maps for AOI or job results in the Workflow Manager client. They are not the individual job MXD versions, that is why they are not displaying.
Your statements with respect to Store MXD are correct. 🙂
Hope this answers your questions,
Michael