Best way to fix this rust?

I have rust in an odd spot in my dart. It looks as if the trunk seal is not working properly and the moisture caused surface rust on both sides, inside the trunk where it is circled in black. It had actually rusted through (circled in red). The metal is not thin, and the spot that rusted through is still strong. I am going to cut the small rusted out piece out and replace it. What is the best way to tackle the surface rust in the trunk?

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