So I have progressed far enough into the Dawnguard story to have been given the quest to find the two Elder Scrolls. I just trudged through the Soul Cairn to find the first Scroll. I went to the College of Winterhold to find the second Scroll when everything started to appear familiar. It all reminded me of the main quest like when I have to find the Elder Scroll! However, I have not even started the Skyrim Main quest as of yet, but have been given the quest "Discerning the Transmundane," which I know is a good ways into the Main Quest. Even the journal entry says that I need to speak to Signus in order to find the Elder Scroll for Paarthurnax!

Will advancing the Dawnguard questline further have a negative effect on the Skyrim main quest?

No, but be prepared to fight Alduin when visiting High Hrothgar the first time. You already have the Dragon Scroll and are at the Time Wound...

The quests intersect at discerning the transmundane, but there is no need to be that far in the main quest at all to achieve the objective in Dawnguard.

It will just make that part of the main quest easier once you get there if it has not already been completed.

Um that wouldn't be the first time, that would be like the third time that the main quest sends you there if you have it and that third time you would be going up to the peak of the mountain.

The first time you go to High Hrothgar you are sent to fetch a certain item.