Anything is possible with computers if you have enough time & money!
The Leonardo uses LUFA to achieve the USB and serial software interfaces. The 32U4 has the internal USB circuitry that LUFA manages. The bootloader code also provides the BIOS table such that the Arduino libraries "sees" serial as a physical interface and remaps the hardware serial to Serial1.
If you have too much time on your hands and want to modify the Leonardo boot loader, start with the LUFA's author blog:
http://fourwalledcubicle.com/blog/2012/08/lufa-and-the-arduino-leonardo/
Ray