Break my game in what way though? As In I cant finish the main quest or will just make it extra hard to do whatever quest I set the stage too because I did not go to the areas or aquire the items required for said quest beforehand?
Unless it was destroy what Mods do like DD or Wars in Skyrim and make AI act differently I think ill take my chances.
When you go to certain places, complete certain bits of dialogue or progress in a quest, scripts are run. These can be scripts that give you the appropriate reward, do special effects or whatever, and these are harmless.
However most of them will enable people, kill some off, disable/enable objects and areas, add the appropriate dialogue and quest items.
If you are on say quest 2, you'll find that the scripts from quest 1 didn't run. So maybe the Graybeards won't even be there when you go to the mountain, they might not have the dialogue required to further the quest, stuff like that. Also, a lot of the quests have conditions, say GetQuestCompleted MQ02. As you haven't technically completed MQ02, the quest won't run.
So yeah, lots of issues. Just do it how the game is designed.