Ken,
Remove inner surfaces is handy when you have merged two or more solids together and you want to "clean up" the surfaces that might be now on the inside.
In the photo below you will see that it shows 4 blocks that were merged together. The end faces are the blue surfaces. To clean up the drawing you would use remove inner surfaces. This clears out the surface on the inside of a water tight model. The are just remnants from the combined parts.
This is only an example but there will be times when you merge say a cylinder to a square and want to get rid of the stuff inside the combined solid.