I think that you are wrong on this one. You can have multiple zend framework application on the same hostname. I.e. i've been using multiple magento's installation on my server in order to try out things. Zend doesn't have fixed file structure as far as i know (one of the reason of my choice of framework)
You can place even place Zend Library outside the webroot folder and call it with something like this:
$lib = realpath(dirname(basename(__FILE__)) . '/../../../lib');
set_include_path(get_include_path() . PATH_SEPARATOR . $lib);
$rootDir = dirname(dirname(__FILE__));
define('ROOT_DIR', $rootDir);
set_include_path(get_include_path()
. PATH_SEPARATOR . ROOT_DIR . '/library/'
. PATH_SEPARATOR . ROOT_DIR . '/app/models/'
);
include 'Zend/Loader.php';
spl_autoload_register(array('Zend_Loader', 'autoload'));
// Load configuration
Zend_Registry::set('configSection', $configSection);
$config = new Zend_Config(new Zend_Config_Ini(ROOT_DIR.'/application/config.ini', $configSection));
Zend_Registry::set('config', $config);