Up to your questions:
1. For a number of reasons the tooltip objects are added to the end of the FORM. This means that they are outside of all other MS AJAX UpdatePanels or RadAjax UpdatePanels on the page, and you should not expect a click on a button inside the tooltip to produce a callback only for the fact that the tooltip's target element is inside an UpdatePanel.
To peform a callback, please follow the approach in this online example:http://www.telerik.com/DEMOS/ASPNET/Prometheus/ToolTip/Examples/AjaxUpdatePanelInToolTip/DefaultCS.aspx
2. As far as we have been able to test, the current download of the ToolTip and the ToolTipManager should update and rebind correctly when partial page updates are made [as long as they are configured properly]. In case you haev encountered a problem, please send us a simple working project that demonstrates the issue and we will provide you with more information.
3. It is very likely that the reason for the behavior is the reason explained in #1 - the tooltip's content area is added to a different place in the page DOM than the tooltip's original location. This is essential for the proper functioning of the tooltip and cannot be changed.
Thus, unfortunately, expecting to use the tooltip just as, say, asp:Panel is not realistic - instead you should use more UpdatePanels to achieve the desired behavior.
We hope this information helps.
the Telerik team