Smart cover/keyboard cover steel holding magnets against the iPad's aluminum back case-oxidation issues
One of the things you could do which is what I did with my smart covers for my iPad 2 and 3 was to put a long thin strip of clear tape ( I used heavy duty clear packing tape cut thin with straight edge and utility knife or an Xacto knife) and placed in along the area of where magnets on the cover attach to the magnets inside the iPad.
This way the cover magnets still catch and the magnet doesn't make direct contact with the aluminum case on outside as the tape acts as a buffer/barrier.
It's the fact that the cover magnets are made from iron or steel and it causes an oxidation reaction when the steel magnets come in contact with iPad's aluminum back case.
You can't do anything with magnets inside of the iPad's aluminum case (if this is leaving corrosion oxidation marks on the inside), but you can create a barrier to keeps this reaction from happening on the outside of the iPad's case from the case's magnets coming in contact with the iPad's alumium back surface.
I am not sure why this is happening as Apple has been covering the different iPad smart covers completely in silicone or leather and this includes covering up the steel magnets in the same material to create a similar buffer/barrier against the steel/aluminum oxidation issue.
But the added clear tape on contact area of the smart cover/keyboard cover on the iPad would create an additional buffer against this as does not effect the strength of the cover magnets against the iPad.