Yes, there are now several options to manually attain the certificate.
There is a "manual" mode, "Here is the file that you need to post, press Enter when you are ready to continue"
There is a "standalone" option. If you don't have a webserver running, it will bind to port 443 and solve the challenge for you.
There is also a "Webroot" option. Enter in your server's webroot and it will automatically post a file to .well-known and delete the file after validation.
Also, the current implementation only changes the SSLCertificateFile directive if you provide your own --key, --csr and already have an SSL vhost for the domain. (This one change is logged.)
There is a "manual" mode, "Here is the file that you need to post, press Enter when you are ready to continue"
There is a "standalone" option. If you don't have a webserver running, it will bind to port 443 and solve the challenge for you.
There is also a "Webroot" option. Enter in your server's webroot and it will automatically post a file to .well-known and delete the file after validation.