Hey Robert,
I had this issue also in the past, but I still can not figure out how to resolve the issue with all of my labels and symbology connected to one layer in the table of contents. For example, I set my anno layer to dynamic, but all of the other layers are there too. I also have a few tools that have to work with feature service layers (search for example), similar to the web map that you posted the example for. I have attached my configuration file. Any quick help would be greatly appreciated. Thanks