You don't need to edit that file, so please, undo the change on that file. If you want to configure your application to use Virtual Hosts. You need to edit the file
/opt/bitnami/apache2/conf/bitnami/bitnami-apps-vhosts.conf adding the linew below:
Include "Include "/opt/bitnami/apps/customphpapplication/conf/httpd-prefix.conf"
Then you can create your Virtual Hosts Configuration at the file
/opt/bitnami/apps/customphpapplication/conf/httpd-prefix.conf without affecting the rest of the Apache Configuration.
Please edit that file with the content in order to move the app to the root of the URL: