One of the first things I learned one summer working in a body shop is that you don't mask around the patch or you will have straight lines that define where you patched. We would always mask off the panel where the patch was located and sand a foot or more out from the patch. We would then paint the area, trying to feather the paint from the patch into the old paint. We had spray guns, so when we had feathered with paint, we would hit the edges lightly with a spray of thinner to help the new paint blend.

Regarding the clear coat, I've used the new spray can clear coats on cars, other than MBZ, with very good success. I don't think you will have any problems, but you might want to spray some on the area you are going to patch before you remove the area to see what it does to any paint/clear coat that is left in the rust area.

Scotty