Currently you can create nested masterpages by setting the MasterPageFile
property in the subpage to the name of the base page. Logically this means that the markup from the subpage will be replaced in the base page, where the corresponding ContentPlaceHolder resides.
Templates in Sitefinity are created from masterpages but they are not masterpages. They are stored in the Sitefinity database and keep references to the controls they contain. Essentially this means that there is no hierarchy in templates, only masterpages.
What happens in your case is that the base template (created from the base masterpage) keeps a reference to the controls you've put in it. However, this is not the case for the sub. It only knows that it is supposed to show the markup of the parent, and there are no controls in that markup - only a ContentPlaceHolder, which is what you see.
Unfortunately this is how nested masterpages work in ASP.NET, and if you want to add a control to the base that is also seen in the template created from the sub, you would have to add it in the markup, not through Sitefinity. In this way the control would be created in the file itself and seen from the sub, not in the database. I hope this makes templates and masterpages a little clearer now.
the Telerik team