My low level is a tad rusty from when I learned the C side in school, but if I recall the not operator resolves as a single Boolean (0 or 1 in true C), whereas compliment comes back as however many bits you put in - a not operation per bit.
In C, the not operator is !
and the compliment operator is ~
For Certbot, I think it’s even further up the chain - OpenSSL. And if you’re installing it to Apache or Nginx, its probably just OpenSSL again.