The getting started page is a mess! Every customer I have been too so far have governance that locks down the team sites to prevent customizations around "Themes" and chanding the "Logo" and "Description". First thing I'm going to be doing is removeing those last two metro buttons from the page completly! I'll post the steps here later….
Figured out how to do this. It is actually a web part and have no configuration values to remove any of the "metro" buttons. In order to remove it from a site, you must either delete it from the onet.xml site definition, or make a call using the client object model to get a LimitedWebPartManager and then delete the web part from the page or fire an event handler after web creation and remove it. May even be possible to hide it in your own master page via CSS.