THe headtube is different with a Integrated headset vs a standard 1 1/8" headtube.. The steeerer on the fork on both is 1 1/8". The headtube on the frame is actualy larger when you have a integrated headset so they can fit the bearings inside.

So for a example a fork designed for a frame with a integrated headset will have a larger base where the crown sits on it so will seamlessly integrate with the headtube gives a smoother look.