SUGGESTION: It would be nice if the user OPTIONALLY could configure the automatic layout, so that it keeps a X pixel/em margin between neighboring tree branches.
PRO: Can help visual readability.
CON: More canvas space is used. Less available.
BUT: As this feature shall be optional, it does not harm those who like the current auto-layout, but serve those who might like some more visual branch distinction.
MOCK UP: I attached a demo map + screenshots, which shows the intended automatic layout, which I achieved by manually dragging the branches apart for the demonstration purpose.