You can do this all in Portal mode simply by setting visibility of the webpart zones or the webparts themselves. Then if you use content inheritance properly the pages will all inherit the master and other content as you're looking for. In fact, you can use multiple page placeholders (for v5 but still relevant) on a masterpage and specify what page template the sub pages use. This is very helpful for weird layouts/requirements.
Also keep in mind if you need to some some authentication items or other more global type items in code, these can be handled within a custom event handler. For instance, capturing the authentication event to maybe find out what user is logging in and assign an account number or maybe to authenticate with another system. Kentico allows you to do all of this without needing to create an aspx page template. Just write your code in the global event handler, it's more efficient than having to write code in an aspx template and is more accessible.