Perhaps I should ask, how do you create a hole or a contour? Prevoiusly I have used Expedition and in that package you simply add a mounting hole and specify its dimensions.
Personally I define the mounting holes as components in the schematic; that way if I need to connect them to a net (such as chassis ground) I can make the connection. Others like to define them as components only in the layout.
There are lots of ways you can do this. If you are concerned about the metal in the inner layers, check your padstack for the mounting holes. you can probably modify it and remove the inner layer copper.
Check your Gerber definintion in the CAM section <File><Cam>(select a document)<Edit><Layers>. You can use multiple layers to generate each Gerber file, and you have a variety of options for what comes from each layer. Board outline has its own selection button so it can be selected indepent from all other layers.