Get the whole idea of a factory bevel out of your mind, it will only confuse you more. There is no way the factory put a 30 degree bevel on your knife, those type of statements are made to keep the masses happy.
If you set a lower angle than what is in place then yes, you will hit the shoulder and if higher then you will apply a microbevel. When using any guided system you must forget the bevel you have now and create a new one to match the tools settings. Start with your coarsest stone and grind a fresh bevel at the angle you desire, make sure you complete this first process with the most accuracy as it is the most important. Once you have created the bevel and used light finishing strokes to reduce the burr you can move on to finer grits to reduce your scratch pattern and increase sharpness.