I think I see what you're saying now, thanks for clearing that up! I have a few ideas that I hope might get you closer to what you're attempting to accomplish.
Since you're using the Template editor to define global controls, you could actually instead define them right on the master page itself. For example, to add a search box, you can register the sitefinity control as follows on your paster page:
|<%@ Register tagprefix="cc" namespace="Telerik.Search.WebControls" assembly="Telerik.Search" %>
|<cc:SearchBox ID="SearchBox1" runat="server" IndexCatalogue="MyCatalog" ResultUrl="~/Search.aspx" LayoutTemplatePath="~/Templates/Public/Search/SearchBox.ascx" />
notice that the SearchBox control has properties that match the sitefinity property editor. The navigation controls are located at /sitefinity/usercontrols/navigation35 and can be similarly set.
the newsletter web controls are registered with this:
@ Register TagPrefix="cc" Assembly="Telerik.Notifications" Namespace="Telerik.Notifications.Newsletters.WebControl" %>
I realize it's not ideal, since if you want your users to be able to make changes to this, they can't using the sitefinity template editor, however since this setup shouldn't be changing often (it's global to the template) I think it would be a good idea to do it this way.
this has the added bonus of allowing you to modify these controls at runtime using the code-behind of the master page. For example, your newsletters module, you could handle the Page_Load event and check which url you are on, and if you're not on the list of approved pages, set the visibility of the control to False.
it's a hack to be sure, but I have used this quite method quite successfully on several sitefinity sites. I lose the convenience of making changes in the sitefinity admin editor, but I gain the full support of the IDE to customize the site exactly the way I want it
I hope this gives you some ideas on how to proceed! If anyone knows a better way to do this, please share as I'm sure it would save me a lot of time as well!