On the SAM the bootloader resides in silicon, you cannot erase it and it doesn't take any flash space. I would think it could be disabled somehow but can't see any reference to doing so.
It will boot from either USB or the UART so there's no need for Arduino to supply another bootloader.
That said with ARMs (or at least LPCs) you can write a "secondary" bootloader if you want to do your own thing, I assume that would reside in flash but I can't see any reference to doing that in the SAM data sheet.
EDIT: It does look like the GPNVM bits can be used to select the boot options.
Rob