You can't use those vars in TI-OS and when you delete them, your calc crashes. Actually, it's about 20 bytes further in memory. Well, the first two bytes of each program contain the length of it. And for a shell program or an assembly program, there is no difference. For a shell program, The first 20 bytes or so contain a real basic program.
Purpose is to copy the two special vars in order to start the shell.
Next to this code, the shell also contains some functions for use in assembly programs. This function is used to call functions in the ROM without having to concern which ROM version is running in the users calculator.