Create a method to prevent parental and causal links to sub-tasks unless those sub-tasks have sub-issues
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.
waiting for clarification
I'm not sure I fully understood the configuration you've described, but Links synchronizer's scope can certainly be limited with "Parent JQL" and "Child JQL" options. If an issue (whether it's in the structure or not) does not satisfy the JQL, it will be completely ignored - which lets you cut out sub-tasks from links synchronization.
More details in the docs: https://wiki.almworks.com/x/lwBg