When the tooltip is behind the modality it cannot be closed by the users. 

You can workaround this behavior by following the script below:

<telerik:RadButton runat="server" ID="RadButton1" Text="Hover"></telerik:RadButton>

<telerik:RadToolTip ID="rttAdditionalFeatures" runat="server" ManualClose="True" Modal="True"
    TargetControlID="RadButton1" ShowEvent="OnMouseOver" OnClientShow="OnClientShow">
    Some text
</telerik:RadToolTip>

<script type="text/javascript">
    function OnClientShow(sender, args) {
        var modalLayerZindex = sender._modalExtender._backgroundElement.style.zIndex;

        if (sender.get_zIndex() <= modalLayerZindex) {
            sender.get_popupElement().style.zIndex = modalLayerZindex + 1;
        }
    }
</script>