It is about control... physical
One of my favorite pieces of modern revelation is D&C 89, but not for what it says about coffee, tea, or tobacco, rather for the reason the Lord gives for the revelation:
Behold, verily, thus saith the Lord unto you: In consequence of evils and designs which do and will exist in the hearts of conspiring men in the last days, I have warned you, and forewarn you, by giving unto you this word of wisdom by revelation—
The revelation know as the Word of Wisdom is given not for health reasons, but because of the evils and designs in the hearts of conspiring men in the last days. What are these evils? In a word, addiction, slavery, and death. In addition to the things that are obviously bad for us, as individuals, there are now even more ways for us to become enslaved to food and beverage. Much of the fruit that we purchase in the grocery store comes from outside the United States, and many of them are hybrid products that can not be grown from its own seed. If I wanted to dry out the seeds and try and grow my own, it would not work, and I would have to purchase seed from a seed manufacturer. High fructose corn syrup, or HFCS, is in the news frequently and has been blamed for obesity, diabetes, and other health issues, and yet seems to be in everything we eat or drink. We as a nation are not blameless, as we sit on our couches and become more and more lethargic, and gain more and more weight. If we ever had to rise up and fight against an oppressive government or force, we would be ineffectual. There is a reason that the Lord outlined how we should eat and drink in D&C 89. We need to be ready and willing to go at a moment's notice in defense of Christ and His plan. We need to be physically fit, which will allow us to stand for that which is right. Many of us can barley stand at all because of all the toxins we put into our bodies.