Consolidate self-signed and Let's Encrypt SSL certificate generation

With Let's Encrypt certificate enabled by default for the new virtual servers, the usual log looks like the following:

So as you see from:

the system (1) first generates self-signed certificate with the bunch of ssl.* files created in the websites home directory like:

and then only after setting up log file rotation, creating MySQL database, re-starting DNS server, applying web domain configuration, re-starting Webmin, re-starting Usermin, saving server details, sending email notification to domain owner finally in the very end it (2) requests Let's Encrypt certificate. Moreover, after generating the Let's Encrypt certificates the system never cares of deleting all those ssl.* files created in step (1).

I wonder if it is possible at all to avoid completely step 1 (self-signed certificate) if we are going to get Let's Encrypt certificate little bit later? If not, then somehow these two steps should be consolidated and the system should clean up unnecessary ssl files generated for self-signed certificate.