The question is: all tasks on the project are managed through Features, but time-tracking is stored in the story. Is it possible to make it so that when adding time-tracking to the story, a record is also created by script in the feature ?
You can automate this scenario with a custom workflow: when a new work item is added to a story, find the related feature and add the same work item there. The latter can be done via the issue.addWorkItem method.