The program which operates is different.
In boot mode (USB interface), the on-chip flash memory modifying program (boot program) stored in a dedicated area within the microcontroller operates. The boot program cannot be deleted by the user.
In USB boot mode, the on-chip flash memory modifying program (USB boot program) stored in the user boot area operates. The USB boot program can be deleted by the user.
Also, when a flash programmer is connected without ID code protection, all user programs will be deleted.