There's no question that HM wins big in Dragonborn, but maybe he wins even bigger than we are told.
When Alduin js thrown forward in Time, the Dragonborn was (I suggest) divided into two selves: the past Dragonborn (Miraak) and the present Dragonborn. (We can see that they are divided from the way that Dragon souls are shared out between them as Miraak's connection to Mundus is amplified by the shrines. Also, both Dragonborns are HM's champions, whether expressly because the present one does the Oghma Infinium quest or implicitly because HM is already observing him.)
Miraak is seeking to enter Mundus in order to unite the two halves of the Dragonborn, but with his half dominant. Preventing this will keep the Dragonborn weak and pliable, so HM tricks the Mundane Dragonborn into slaying his other half: the Mundane Dragonborn so readily acquiesces because his other half already serves HM in Apocrypha.
As an added bonus, HM gets to keep the true nature of his deception secret.
It is possible that the Dragonborn is also himself a 'book' in the sense that he partakes of the nature of the Elder Scrolls himself: indeed, he can read them without training, and shares their ability to stand outside normal history. Indeed, it could be argued that the Elder Scrolls series is so named because these scrolls have the capacity to manifest both as books and characters. If this is so, then the Dragonborn is not so much a rebellious person as a rebellious book ... which would explain HM's otherwise incomprehensible fury.