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Dfu-util is one of those "user space drivers", so if you have a nonstandard protocol you'd have to add it directly to dfu-util. There's no intermediate API.

It's not easy to set up a fake or "remapped" USB device on most OS as far as I'm aware, if you were trying to write an adapter program that modified USB packets.

That's two different problems really. You mostly use libusb when you own the application part too, think of an utility to burn firmware into phones or something like. You can also make a userspace driver for some device classes, like input. If you combine the two, you can let the rest of the system use the device without knowing what it's driver is.

dfu-util actually also just uses libusb under the hood! Any class or device that doesn't have a driver baked into the OS can be implemented like this. And if you'd need the DFU functionality in a different application, you may be able to just simply link parts of the dfu-util tool into your application