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This was my suspicion. As I am also using composer/installers, I was hoping to piggy-back the useful feature to change the destination of the packages and write the modules into a more Drupal-like destination, such as sites/all/modules/contrib/ - instead I will just copy these "rogue" modules into the appropriate directory using post-update-cmd.

Is this the approach you have been taking as well or is there a better way?

I have converted an existing drush make project into Composer and will be testing it out in an upcoming project, using some of your very useful Composer plugins. Thank you for your work in this area, I really see it as being a more linear way to develop and build Drupal projects.