When you create a template or open an existing template you will see a window that looks very similar to the Control Panel. However some options, like Files with Special Processing, are not included in the template definition as they are Package specific information which cannot be generalized in any meaningful way.
If you have created a template by copying an existing Version or Patch the 16.3.1 Template Installation Options displayed will reflect the base settings and options. You may choose to review the template and hide or highlight specific options.
To understand how values and appearance are controlled by templates refer to 16.3.2 Template Option Values and Appearance.