I would second both of those. Another thing that you could do would be to edit the axidraw control script on your computer and suppress the error message. (I can point the way if you would like to do that.)
Another approach would be to add some “out of band” data. If you right click on an object, you can view its Object Properties in the XML editor. There, you have a “description” field that you can type into, and save any notes that you would like to associate with the object.
Beyond that, it’s not a bad idea to add a feature into the software to support named documentation layers. I’ve opened a github issue for it, here: https://github.com/evil-mad/axidraw/issues/29
