read the manual 
but like most things in computing if it can’t find a configuration or you don’t tell it what you want to do it’s not going to figure it out by itself
In the case of certify it uses your IIS configurations to find a list of domains. lets-encrypt-win-simple gives you a bit more flexibility however - it won’t figure out who’s connecting to your server as it also looks at IIS bindings or waits for the user to enter the right domains.
If you have customers that access your web server without a specific binding and hostname etc that’s a challenge for you to sort out
Andrei