Workaround in OnClientBeforeClose (commented):

<telerik:RadWindowManager RenderMode="Lightweight" OnClientClose="OnClientClose"
     OnClientBeforeClose="OnClientBeforeClose" Behaviors="Close, Move, Resize,Maximize"
     ID="RadWindowManager" runat="server" Width="450" Height="400">
    <Windows>
        <telerik:RadWindow RenderMode="Lightweight" ID="RadWindow1" VisibleOnPageLoad="true"
            Title="Wikipedia" _NavigateUrl="http://www.wikipedia.org" IconUrl="wikiFavicon.ico" runat="server">
        </telerik:RadWindow>
    </Windows>
</telerik:RadWindowManager>
<script type="text/javascript">
    function OnClientBeforeClose(oWnd, args) {
        //workaround:
        //oWnd.get_popupElement().style.visibility = "hidden";
    }


    function OnClientClose(oWnd) {
        debugger;
    }
</script>

The IE iframe module crashes, most likely because of the fact that events do not bubble to iframes.

The ContentTemplate is designed as a container for server controls, so you would need to declare and use a RadWindow with a ContenTemplate (even blank) for this to work as expected. The ContentTemplate element is not created upon client-side setting at this point, so having a content that is not where it is supposed to be may break the control afterwards (e.g., if autosizing is used).

A workaround is to create a dummy content template that can alleviate most issues:
var wnd = radopen(null, wndName);

//create an imitation of the ContentTemplate
if (!wnd.___customContentElemCreated) {
$telerik.$("iframe", wnd.get_popupElement()).remove();

var cElem = document.createElement("div");
cElem.setAttribute("id", wnd.get_id() + "_C");
cElem.style.display = "";
cElem.style.overflow = "auto";
cElem.style.border = "0px";
wnd.set_contentElement(cElem);
wnd.setWidthDockMode(wnd.get_width());
wnd.setHeightDockMode(wnd.get_height());

wnd.___customContentElemCreated = true;
}

wnd,set_contentElement(theNewElem);

As a workaround you can manually display the loading panel as per this KB - http://www.telerik.com/support/kb/aspnet-ajax/window/details/custom-loading-sign-for-radwindow

When the Lightweight render mode is enabled and you set large text in any of the dialogs of RadWindow, part of the text appears outside of the window.

You can workaround this issue by overriding the styles of the dialogs. Below you can check a possible approach for RadAlert:
    <style type="text/css">
        div.RadWindow {
            overflow: auto;
            height: auto !important;
        }

        .rwDialogMessage {
            padding-bottom: 30px;
        }
    </style>