If I manually modify ServerName and ServerAlias for a particular website in httpd.conf, will those changes be permanent, or will updates break them?
If you are running EA3 then those changes will not be preserved. If you want to make any custom change then make it in /var/cpanel/userdata/username/domain.com file and then run /usr/local/cpanel/bin/build_apache_conf and then restart the Apache.