You'r right, the rot13 command is a shell wrapper around:
`
exec /usr/bin/caesar 13 "$@"
`
Forcing the key to be 13. You can obviously invoke /usr/bin/caesar with any of the 25 keys.
The use of rot13 was just an amusement in this case given its vintage. Replacing rot13 with any other simple stdin/stdout transcoder should be simple to do via the socat invocation, eg base64, a sed replace command, gzip/gunzip, even an actual symmetric encryption protocol like AES, etc.