A common misconception is that a DropDMG layout is like a document that stores a recipe for how to build your disk image. With that line of thinking, adding a file to your layout should cause that file to be copied to the disk image whenever that layout is used. However, this is not how DropDMG works.
Instead, the content and presentation of your disk image are specified separately. The layout controls the presentation. When you add a file to the layout, this creates an icon that you can drag around so that DropDMG knows where to position it in the mounted disk image window. Adding a file does not create a reference to that file or tell DropDMG to copy the file when creating the disk image. All it does is tell DropDMG where to put the icon for a file with that name. Because only the name matters, you do not have to re-add a source file to your layout if you move the file or modify its content.
The contents of the disk image are always determined by the source folder that you drag onto DropDMG (or pass it via script). So, to add a file to your disk image, you need to add it to the source folder. The source folder can have more or fewer files than are mentioned in your layout. You can also use different source folders with the same layout.
This separation between content and presentation lets you create different looks for disk images with the same contents, for example beta versus release versions of a software product. It also lets you use placeholders and variables to apply the same layout to multiple disk images that have different content, for example multiple products from the same company.