The 'Apply Auto-Mitering' option is turned on by default in order to avoid errors when you create 2 or more flanges in the same operation. That behavior cannot be changed.
Notice that if the option is turned off manually, it may lead to a 'Body intersection' or 'self-intersection' error, depending on your geometry. Having the option turned on should not alter the flanges unless there is body interference.
If you have a good reason to have that option turned off by default, you can post an enhancement suggestion in the Inventor IdeaStation forum:
http://forums.autodesk.com/t5/Inventor-IdeaStation/idb-p/v1232