“Include all” does not equal “Include” + selecting all link types.
- “Include all”: link types from all installed process templates will be shown to the users.
- “Include” + check all boxes: Only the links types in the current process template will be shown to the user.
In my experience, “Include all” is never a good option for a work item link filter. It will only serve to confuse users and break reports. But when working with the Process Editor “Include” restricts your selection of link types to only include those specified in you process template. If you want to use link types from your template and some of the system defined link types (like parent/child) you will have to edit the XML markup manually.