I wish I knew more about the USB chips in the different Myth carts. From the client software for burning menus/saves/games (look at madmonkey's client code) you can see sequences of Myth commands sent to do things like activate the menu flash for reading/writing, activating the game flash for reading/writing, and activating the save ram for reading writing. So I would conclude that is SHOULD be possible to dump carts across the USB if it can be done from the console side by making a USB sequence that matched that used from the console.
I wished I knew more about the USB side of things as well to help madmonkey make his client a little better... maybe try a few experiments like retries on writing games when the game flash randomly fails. That's a BIG problem on the N64 since writing 512Mb games is almost impossible for some folks due to those random block fails. I've been able to burn Conker to flash ONCE in many dozens of attempts due to random block fails.