Per ASME:
Flatness comes into play in with the "To or Thru Rule".
[ul]
[li]If the stack goes to a surface, the form of the surface must be accounted for in the stack.[/li]
[li]If the stack goes thru a surface, the form of the surface is automatically included in the limits of the dimension.[/li]
[/ul]
Think of two flat washers held together. If you can fit a feeler gage between them, you are checking surface to surface. Flatness would control the amount of gap.
If you set a micrometer to the outsides of the two washers, the flatness would already be included in the dimensional limits of the two thickness'.