Yes, a 404 is an http error Not Found. You might try
sudo certbot certonly --apache --dry-run
If that works remove --dry-run to get a production cert
The --apache plug-in will insert temp code into your Apache config for handling the HTTP Challenge.
Your first post showed some problems with Alias statements so without seeing your VirtualHost config it is hard to say for sure what will work.
This subfolder gets created by Certbot and removed after the challenge.