As I understood it since it was made clear that there is no 'innerbot' - Kup's spark and brain have been interfaced with his new body in a similar way that the inner bot would interface with a Pretender shell.
So If you break Kup open you will not see an inner bot but his severely damaged positronic brain and spark chamber interfaced with his new body's (shell) electronic brain which compensates for the damage making Kup 'normal' again.
He now has a regular Transformer body but his brain (and spark) is plugged into it using Pretender technology rather than how it would be by conventional means.