There are more differences than just the addition of boxing. The frame rail is different. The hardtop has the body mount supports welded between the upper and lower rail and the rail is lighter gauge. The boxed frame has the mount formed into the rail and is heavier steel.
I won't say it can't be done, but you might want to explore all options of repair first. Unless the entire frame is bad I would opt for repair. Having just gone thru a level 2 inspection to register my 64 SS in AZ I can tell you that the frame number at some point in time will be looked for. In AZ if the frame has been changed they will vin the car to the frame or assign an AZ vin number, neither of which will keep it numbers matching.
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Philip #42
1964 El Camino
1964 Malibu SS