I haven’t tried this myself but in theory Certbot has options such as --apache-server-root, --apache-vhost-root etc that let you tell it where to find things rather than using the OS defaults. Type certbot --help apache for more information.
Also, if you’re installing your own Apache from source, you might be better off using certbot-auto rather than installing from yum, since the latter (as you saw) will install a second Apache as a dependency, which might confuse your startup scripts as they both try to listen on the same ports 