Status currently if you map a LabelSetImage it is mapped as an normal image with (NN interpolation), so after mapping it has been converted in an normal image showing all labels.
At least we should implement in the mapping helper the full support for label set images to handle them correctly. Or we should take the extra way and introduce a service interface for mapping data to decouple this and allow (new) modules to register registration mappers for there data types on there own (and to define properties (as a servive property) to overrule if they have a more specific implementation then others.
Remark: Till this task is fixed LabelSet images are excluded in the mitk::RegistrationHelper::MaskNodePredicate(). Add it when fixing this task, to allow the regstration plugins also to detect labelset image based segmentations