I'm thinking of writing programs into the UART serial on Arduino Leonardo instead of builtin CDC serial on Leonardo to get rid of the if (!Serial) debug nightmare.
Please explain, what the debug nightmare is with this command sequence. I don't have nightmare because of it.
Is it possible through changing the boot loader or simply burn Uno boot loader onto it?
No, not without modifying it. I guess you could modify an optiboot loader to work with the ATmega32U4, but how do you want to upload the sketches then? Using a separate USB2serial converter? Do you know the necessary circuit to do so?
Which leads me to another question. Just curious, is it possible to start boot loader on an alternative serial port than 0?
You don't "start" a bootloader on some serial port but the code in the bootloader reacts on commands from a specific serial port a few moments after a reset. Do you really understand the concept of a bootloader?
Please explain what you want to achieve? Not how you want to achieve it.