The exoskeleton is a outer layer that is generated by the internal Endoskeleton or Protoform, which is what allows transformation. While the Endoskeleton morphs, constracts and expands, the Exoskeleton can shift around, join together and split apart, all while connected to the Endoskeleton.
It also exists to provide protection and can be modified for greater strength. At its bare minimum it is immune to weaponry that rely on things like gun powder for propulsion.
When an alternate form is chosen, an exoskeleton will take on the characteristics of that form, this is because the Transformation Cog, quickly figures out the specifics of the transformation.