If it were my box and I wanted to save the patina, I'd use steel wool as well. If I didn't want to save what's left of the original colours and rust, I'd have it sandblasted and I would use a product called POR-15. "Paint Over Rust" is a product that I've used a lot and it does a fantastic job of sealing and converting rust so that it does not get any worse. Fantastic stuff. Though, it doesn't like paint, so you'll have to remove the lose paint and flaking rust first.
If there is a dime sized hole in the box, chances are with blasting or rust removal it will get bigger, so you're likely going to have to use some body filler to fill in the hole. I'd use the stuff with fiberglass strands in it, much more rigid than just straight Bondo.
Clear lacquer will seal in the patina but probably won't last as long especially if it's a user.
Unless you fully restore the box, taking all the old rust and paint off, cleaning it really well, using some POR on the rusting spots, and priming and painting it, you'll never stop the rust, or even the patina that's on there.
I like things to look old too, but there's a question you need to ask yourself if it's going to be a show piece or a user.
Just my two cents, hope I helped.
YV
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