I do not know of any instance of daggerfall side quests interfering with daggerfall main quests
It is probably possible because daggerfall has a lot of bugs and could probably happen if a side quest takes you to the same location as a main quest while both occur simultaneously but as long as you only do side quests when you are not working on a main quest that is not an issue
But the quests for Skyrim seem so confusing that it is annoying to try to figure out what quests to do in what order
I did the mages guild quest then started the thieves guild quests then got confused because so many other quests would pop up
I am trying to avoid the main quest until I complete a bunch of other quests that do not prevent quests
I do not want to pick sides in rebels vs main empire for example and so on