Michael,
Esri has now created Enhancement Request ENH-000108149 for these issues.
It is a roll-up of other bugs and enhancement requests that had been closed as "Expected Behavior" because users should plan ahead for all the layers needed on the initial publish of the service, creation of web maps and applications.
Example:
NIM099148
NIM085436
BUG-000092554
BUG-000093880
ENH-000094254
ENH-000080928
I hope I don't make any mistakes, forget anything, have any boss of me change their mind after that initial publishing step.
That perfect workflow scenario would seem to only work for a demonstration but even that would be frustrating if "something came up" while preparing the demo.
I'm looking forward to the fix for this ASAP.
-Bill