Hey there! I'm a Toponaming developer on FreeCAD and I have taken interest in fixing some TNP issues in addons.

The reason why you are still having TNP issues in a2plus, but not in the actual FreeCAD workbenches is because you are using
strings for element references (like Edge1/Vertex2/Face3).

To fix this you need to use a Property Link property (such as PropertyXLink, which I recommend the most)

The copies of shapes that you create with your addon do have TNP protection by default, so nothing needs to get changed there.
Also retrieving elements like Edge[4] in python causes hasher mismatch warnings, to fix use the getElement in the Shape property of parts [like part.Shape.getElement("Edge54")]