Frank, does this mean you put your packages, stylesheets and palettes in Workbench? Is this actually seamless or convenient? It must mean that you do all of your development within Workbench and use straight Mathematica only with the deployed result.
What happens if while using the application in regular Mathematica you find you want to update a routine, or stylesheet or palette? This means that you either have to go up to Workbench to make the change, and rebuild all the documentation even if you haven't changed it, or you can make the changes in regular Mathematica but you must remember to copy the changed files up to Workbench. You have two copies of all these items and must take care to keep them in sync.
I DO NOT put any packages, stylesheets or palettes in Workbench. I leave them all in the deployed application. (I do put the init.m file in Workbench 3, but that's only because it doesn't work if one doesn't deploy some non-documentation file - a definite bug as far as I'm concerned.) Workbench will access all of these deployed files. There is only one copy of them. They can be edited in regular Mathematica and all of the development can be done in regular Mathematica. I only go to Workbench when I want to change or add documentation, which is not that often.
To me it seems much simpler. But to each his own.
