When a batting manufacturer gives recommended quilting distance on the packaging they mean in all directions. So your border quilting plan will not satisfy the minimum quilting requirements. You can, of course, ignore that and go with your plan to only ditch your 2 x 6 rectangles and take your chances. You may be just fine and won't get migration or lumpy spots within that 2 x 6 space. There is really no way to know for sure as there are so many variables, not all washing machines agitate the same, front load or top load, machine dry or line dry.
I have ignored the minimum requirement on long narrow channels. Like say an inner border that only measures 1" I have simply ditched the border and not put any quilting in it and have not had any problems. Chances are you won't either. But if you are truly concerned, then you need to devise a quilting plan that goes into your 2 x 6 bricks that leaves no space measuring bigger than 4" in all directions, top to bottom, side to side.