With PHP 5.6, 5.6.40, and 7.2.24 installed on CentOS 7.8.2003, and “Highest Available” selected in Virtualmin > Server Templates > PHP Options > Default PHP Version, PHP 5.6.40 was assigned to a new Virtual Server.
In addition, when the virtual server’s PHP version was manually changed to 7.2.24 in Virtualmin > Server Configuration > PHP Version, all PHP pages returned 404 when running in PHP-FPM execution mode. (They worked properly in FCGId mode.) This happened regardless of whether there was a DirectoryIndex directive in .htaccess, and applied to subdirectories as well as the root directory.
Manually setting the template to PHP 7.2.24 as the default version and re-creating the virtual server created the virtual server properly.