I've reached a point in Dawnguard where I need to find Septimbus to find the Dragon Scroll, though I read that this is the same quest as a later main story quest (which I haven't done any progress in but the first couple of quests). The wiki said that it should be fine if I went ahead and did the quest now and it would just skip over the main quest Elder Knowledge when I get to it, but I plan on catching up the main story quest to get to it so I don't get confused later on. My actual question is that I was wanting to know if there are any big changes that happen if the storyline gets progressed that far (changes to cities, quests becoming undoable, etc)
The main quest will progress normally. I did the Dawnguard questline before the main quest on one playthrough, it worked fine. After all, the only thing connecting the two questlines is the Elder Scroll.