I was able to fix it myself.
The problem was probably the location of the javascript. Now I have in the
<script type="text/javascript">
var $l = jQuery.noConflict();
if (window.navigator.standalone) {
$l("meta[name='apple-mobile-web-app-status-bar-style']").remove();
$l('#in_web_clips').show();
}
else {
$l('#in_safari').show();
}
</script>
and at the end of the file (in the footer)
<script type="text/javascript">
if (window.navigator.standalone) {
$l('#t3-mainnav').css('padding-top','+=15px');
$l('.menutitel').css('top','+=15px');
}
</script>
And it works like it should. My container is pushed down by 15px, and looks exactly like a regular application. There is no animation or effect (e.g. I don't see the container being pushed down).