Real life parts need clearance to be assembled. They aren't assembled face to face (flush). This clearance may be 0.001 inch or 0.100 inch. Many times in Inventor, I am forced to either 1. constrain to mid planes of each part or 2. remember the design clearance and type it in to offset the mate constraint.
In other software (SW, NX) I can choose two faces of one part and center it between 2 faces of another part. Or I can choose a plane and center it between 2 faces.
I've been using Inventor full time for a year now after 14 years of NX and 1 year of SW, and its clear that this constraint is needed. My current workflow has me adding planes to use for constraints.