JavaFX 3D and Java3D are 2 distinct APIs. Moreover, Java3D 1.7.0 doesn't use the javax.media namespace. javafx.scene.transform.Transform and javafx.scene.shape.Shape3D come from JavaFX 3D and cannot be used in Java3D. Therefore, you cannot use jfxrt.jar instead of j3dcore.jar and vice versa.
-So what are the intentions from the Point of view of JavaFX? Is the idea that only JavaFX be used going forward?
-What is the reasoning suggesting jogamp's Java3D 1.6 with AWT and SWING instead, being the original approach?
I don't really understand the questions so maybe this doesn't answer them but JavaFX is developed by Oracle.
Jogamp Java3D has nothing to do with Oracle or JavaFX so the Jogamp community does not have any insight into the plans for JavaFX or JavaSE.
In my humble opinion, OpenJFX/JavaFX 3D is a lot less capable than many third party libraries. If you really want to use OpenJFX/JavaFX with Java3D, you can try to put a Canvas or a JCanvas into an OpenJFX/JavaFX SwingNode. If it doesn't work, you'll have to choose between OpenJFX/JavaFX + OpenJFX/JavaFX 3D and Swing/AWT + Java3D.