The problem is not that the firewall will rust, but galvanic reaction between SS and alu causing alu to corrode. Coating the SS (not neccesarily the alu) is essential to prevent this.
 
So by that logic, I'm thinking mask off the firewall with exception of the aluminum contact points, and shoot a good primer, correct?
 
I dunno about primer, but I'm going to shoot that intumescent paint. I'll use whatever primer they suggest.
 
So by that logic, I'm thinking mask off the firewall with exception of the aluminum contact points, and shoot a good primer, correct?
No. The more exposed area of SS, the higher is the current density, leading to higher risk of galvanic corrosion on the aluminum. In saline environment SS is as bad as copper regarding galvanic corrosion, and all of it should be coated. The kind of coating doesn't really matter as long as it sticks and is an electric insulator, because all you want to do is to reduce the exposed area to a minimum (there is no need for corrosion protection of the SS).

If you are not living/flying in coastal areas, SS and alu is a safe combination and no corrosion is likely to occur. Copper will cause galvanic corrosion also in non-saline environments, SS will not.