The controller_list is included in config/controllers.yaml of the moveit_config package and contains 3 controllers. One for all joints (arm and positioner) and two for the arm and positioner individually. This is the same approach as found in the dual arm motoman_sda10f_moveit_config package. The latter two controllers have non-empty names and that seems to be a problem based on the issue that you are referencing. If I, however, remove the last two controllers, so that only the unnamed remains I get the following error when I try to execute a planned trajectory (in simulation):
[ERROR] [1550792465.767458570]: Joint trajectory action failing on invalid joints
[ WARN] [1550792465.767995973]: Controller failed with error code INVALID_JOINTS
[ WARN] [1550792465.768094358]: Controller handle reports status FAILED
I do not have experience with multi-group systems in ROSi and could not find much except for existing multi-arm systems to go from. According to this tutorial, “A non-empty “name” parameter may be required if multiple robots are being controlled, to provide separate namespaces.” Naming the controllers is, however, apparently an issue as stated here: https://github.com/ros-industrial-consortium/bezier_examples/issues/2. Could a possible solution be to push the FollowJointTrajectory server down into a namespace (e.g. remap it)? And would I have to spawn two FollowJointTrajectory servers, for arm and positioner?