Thanks for sending in this question, I have actually submitted this as a possible bug to our developers. It appears that the LayoutTemplate does not get read in the Page Templates application, instead it renders the ASPX/ Portal engine mixed type as a normal portal page. You can even see this by clicking the edit layout button in the design tab and then adding a webpartzone in the UI. It does not add the webpart zone to the template, instead it adds it to the page template item in the database. I have sent in a bug report to see if this is by design, not yet implemented or some kind of bug here.