In thinking about your question and any reason not to do it. No there isn't. However, I just finished a throw with somewhat similar situation. I quilted in the ditch a throw size that had large rectangular and square shapes in it. Shapes are like 16x12", 16"x16" etc. 12"x8" etc. You get the picture. I then went back and quilted a grid design in each of them. The only problem I had was to keep the layers flat and work out any puffiness in a uniform way across the section. I even put straight pins in front of the walking foot to make sure any excess was evenly distributed. This is most likely a similar situation you may find.