When we do a project and want to make it into a template, we have a few issues.
First, the template only “grabs” the incomplete tasks, which isn’t helpful.
Second, if we duplicate the project and make all the tasks incomplete, all the people assigned get notified and panic and ask questions.
We don’t want to make a template before doing the project because we always add things as we go, so it’s best to make the template after completing the project for the first time.
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Your workaround is the best one that I know of, with the clearly unfortunate side effect that you mention.
If you don’t need the Assignee or Collaborators in the template, then in the Duplicate dialog un-check those checkboxes.
If you do need them, then if you duplicate, then immediately create the template, then you can remove those people with a batch multi-select action. If you do it quickly enough, you might inhibit the notification, but regardless you’ll be able to unassign or remove as collaborators.