We've found that Archimate Stereotypes won't add to a custom Toolbox using the "Edit with Profile helper", "Add Stereotype". We can select the Archimate Stereotype from the model, but it won't add to the Toolbox.
What does work, we've found out, is to use "Add Item", and then manually type in the fully qualified Archimate stereotype name.
However, this does nothing to help us with the issue that we can't properly specialize from the Archimate Junction stereotype. Even simply creating a new stereotype, specializing from the Archimate Junction, and extending the Junction metaclass, result in a stereotype that is missing the "junctionKind" property. Adding our own Tagged value "Junction Kind" (in which we want to include XOR, beside AND and OR) also, weirdly, does not end up in our stereotype. The resulting stereotype, when used in a diagram, also is of type "StateNode" instead of "Junction", and is missing both the "junctionKind" from the Archimate Junction, and our own defined "Junction Kind".