Thanks a lot for taking the time to investigate and to write down this answer! All this is very enlightening.
Since this seems to be a bug in Ember itself, do you need me to file an issue or have you done this already?
As far as my project is concerned, I cannot work around this by removing .extend() because I need it for a polymorphic hasMany relationship. See my other post about this:
Polymorphic hasMany relathionship with ES6 classes.
Others might also need .extend() to include mixins. I guess the right solution for the time being is to rewrite the super class without the ES6 class syntax;