About your first question: One of the next DataFX Version (I think it will be 8.2 and the plan is to release it in January) will contain support for TestFX. By doing so you can write tests for a Flow or a controller and inject test implementations. You can find an example in my JavaOne slides about Testing with JavaFX:
http://de.slideshare.net/HendrikEbbers/test-driven-development-with-java-fx (the DataFX part starts on slide 34)
About your tree / workbench problem:
The next DataFX Version (8.1 and it will be released next month) will contain a message bus to communicate between different flows. In your example the tree will be one flow and the workbench another one. When clicking on the tree node in the menu you can send a message / update to the workbench flow to trigger a specific action.