pico:
I always got the impression the emulation of USB devices was a bit of an afterthought with the selection of the 8u2/16u2 chips, the prime driver of the change being manufacturing cost. But this business about the firmware in the chips not being legal to clone is also intriguing...
It was. It's not "illegal" to clone the u2 firmware, but since it's not a dedicated USB-to-serial IC (it's just a micro with support for USB client mode), the developer is responsible for coming up with a valid USB vendor ID. The USB Forum assigns these, so you can't just make it up, and it's against USB's terms and conditions to use another vendor's ID. (This is how they ensure the device IDs are globally unique -- by assigning the vendor ID and delegating the responsibility for the device ID uniqueness to the vendor. That breaks immediately if multiple vendors get to share vendor IDs.)
Vendors have to pay (I think it's $2000?) for a unique vendor ID, and it's not permitted to sub-let them. So the clone manufacturer is obligated to buy a vendor ID of their own and program the ATmegaXXu2 with their own IDs. Doing so makes the device unrecognizable to the official Arduino driver (since its keyed to the vendor + product ID pair by USB's design). You could always hack the driver to include your own IDs and distribute that, but if you have no ethics, it's easier to just steal Arduino's valid IDs and hope for the best regarding potential ID collisions.