if you have issues with sub-task type issues there's no way to pull those sub-tasks and any child or resulted in linked issues into a structure without structure creating child and resulted in links for all sub-task tasks of those parent issues. It appears that any configuration of the links synchronizers will results in the sub-tasks getting child and resulted in links to the parent issue. If this is true, I propose the following feature request.
In the Links Synchronizer, create a sub filtering feature that uses the logic of: "don't create parental or causal links for sub-task type issues unless the sub-task has a sub-issue"
This would fix the two problems mentioned in the description. First, sub-tasks would not get parental or causal links to the parent level issues. Second, if a sub-task gets sub-issues by nature of parental or casual links to them, where they're acting as the parent or caused by link direction, those linked issues will appear in the structure.