Yeah, I would agree that the negative habits and tendencies are there mostly due to the stutter. However, those you got more control over than you do your stuttering. And the more time passes that these negative tendencies get reinforced, the harder it becomes to undo even if you become fluent. Look at it this way: The more voluntary control you exhibit over your habits and tendencies and other areas outside of stuttering, the more you strengthen the brain areas and processes related to voluntary control. This positive effect is bound to trickle down even to your speech along all else.