You don't see any of this when the flares are completely on but here is what goes on underneath. I seam sealed the block off plates which is pretty ugly so I shot the area with color matched paint. Your rocker panels are not even close to sealed from the factory so really you're just preventing corrosion. The inside of the rockers is hosed down with rust preventative when done. The block off plates are stronger than the rocker panels.
The red color in the picture is a reflection from my shop light.