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Under the current architecture this is not quite possible as you want it to be. You can always use one master page and out of it create many templates, by using duplicate template. However all content place holders have to be defined on your master page. This leaves you the possibility to just define the layout of those cotnent place holders though different themes. I gues you can put display: none
style rule to content placeholders you do not wish to show in different themes.
The new layout editor of Sitefinity 4.0 will allow you to do exactly what you are looking for. Even add new layout holders through the UI, as opposed to only being able to define them in master pages as in Sitefinty 3.x versions.
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