I agree with Tim. Gun cases are for transport, NOT storage!!
One thing I do use for guns that stay in the back of the safe is a silicone treated, nit gun sock. It breaths, protects from safe hickeys and protects from rust by its treatment. At times I have used them and a hard case for short term storage with no problems.
The rust spots can be easily removed with a real copper penny and a good gun oil. Apply the oil to the rust and using the side of the copper penny to "scratch" the rust off. As if you where scratching a scratch ticket for the lottery. The copper is softer then the steel, but harder then the rust and copper will be left in the steel where the rust pitted the steel. After wipe the steel with a clean rag with more oil and the rust will be gone.
CW