Isn't Akatosh something to do with Time? I might be misremembering, but if so I totally don't see anything wrong with, like above, the inclusion of Time Travel somehow... I know Martin makes references to his dark past with Daedric scholarship, so I *suppose* there's nothing in canon (that I know of-- haven't play dragonborn, so...) to say that Martin couldn't have been somehow warped back into the past following the end of Oblivion, became obsessed with gaining power, and actually started his own bloodline...
A few problems I DO see with that...
- Is Miraak actually recognised as a Nord in-game? As I say, not played DB, but I suppose we could separate the game-design from the plot-design if we really wanted...
- How did the first DB come about? I can't recall reading anything about it in the main game, and again with the DB thing, so... :
: Paradox works fine for me 
So yeah, not something I'd actually believe, but.... this IS TES, haha, so you know... We've already had the "All contradictory endings are true!" scenario, so, "Oh that guy went back in time and became evil..." is kind of believable 
(Oh, or maybe Miraak is our Dragonborn... ::Intentionally plants the seeds of crazy discussion::
)