Two bootloaders would make little to no sense IMO, rather one that supports 2 protocols.
In fact the current bootloader is based on the generic
SAM-BA bootloader for SAMD21 devices. It supports both USB and serial protocols. Either way you have to put the board in bootloader mode or nothing happens.
The USB is there to make life easy, why bother with serial which is slower and requires additional components?
I would propose not to get stuck into naming convention debates, SerialUSB is very specific IMO and it aligns with the Arduino M0 standard. When there are multiple serials, they start to be named after this convention: SerialUSB, Serial, Serial1, Serial2 .... You can look in the definitions of the M0 package to see how Arduino did it. You could actually rename it and switch Serial with SerialUSB if that's what you really wanted, but I prefer to stick to a convention that will likely produce less stress to those switching between boards based on SAMD21 where 1 name can mean multiple different peripherals, would be a very confusing world.