It doesn't matter. One you need to be past the Horn of Jurgen Wind Call to do the main quest for Dragonborn. Also you only get a few extra lines of dialogue from Mirrak if you beat the main quest. --- http://www.gamefaqs.com/boards/615803-the-elder-scrolls-v-skyrim/62287165 - restored faith in humanity. 3/13/2013, shipment date
theres a few lines of dialogue that are different. but no it doesnt matter.
personally i think it fits better storyline-wise before the end of the main quest of skyrim. i see Dragonborn as the dovahkiins journey to realize his full potential as dragonborn to defeat alduin . it fits neatly into the narrative imo. --- Gamertag: Clonedzero