It depends on the nutrient in question.
No, not really. Vitamin D in particular (like all fat-soluble vitamins) is not hard to overdose on.
most people are consuming too few micronutrients
I'd probably phrase it like this: almost every person will benefit from increased consumption of some set of micronutrients. But the issue is that this set is different for different people.
Take iron as an example. Some people need more iron in their diets. But some people need less. Can you recommend more iron to some person X not knowing anything about him or her? No, you can't.
Vitamin D is actually pretty difficult to overconsume (at least, accidentally -- if you wanted to suicide by Vitamin D, it'd be a long and annoying process). According to mayoclinic, you'd need to consume around 50,000IU daily for several months to start getting into Vitamin D toxicity.
I completely agree with the rest of your post.
Eliezer and I have put together this first pass at a recipe for DIY ketogenic soylent--or, as he prefers to call it,The Mildly Surprising Super Ketonic Dietary Replacement Weight-Loss Fluid - It's Not Food, It's Dietary Replacement Fluid!(R) (I am not in full support of this particular preference...)
So let's play Make a Prediction. It seems more likely to be useful than "free associate with why soylent/ketosis is awesome/stupid". Imagine that Eliezer has around a week's worth of infinite willpower (that can only be spent on resisting food cravings etc.). Further, imagine your crystal ball shows you that a month from now, he hasn't lost any weight. What does it tell you about why?
Ketogenic Soylent v1
1 scoop Gold Standard whey protein
1½ tsp calcium citrate powder
1 tsp creatine
½ cup+1 tbsp ground flax
4 tbsp Hershey’s Special Dark cocoa powder
2 tbsp lecithin
⅗ tsp potassium citrate on day 1, increase gradually to 1tsp by day 5, don’t exceed 2tsp
½ tsp iodized salt
⅛ packet Emergen-C
⅕ cup olive oil
1¼ tbsp flaxseed oil
⅗ cup MCT oil
Sucralose to taste
We might need to add water to get the consistency right.
Pills
1 capsule vitamin D supplement/day
2 Opti-Women vitamins per day
1 capsule MSM
Totals Per Day
Calories: 1866
Fats: 193.5g
Carbs: 12g
Protein: 54g
Fiber: 25g
Biotin 250mcg
Calcium 150mg
Chromium 120mcg
Copper 2mg
Folic Acid 600mcg
Iodine 200mcg
Iron 18mg
Magnesium 75mg
Manganese 5mg
Methyl-Sulfonyl-Methane 1000mg
Molybdenum 70mcg
Niacin 20mg
Pantothenic Acid 20mg
Potassium: 5g
Riboflavin 20mg
Selenium 70mcg
Sodium 3g
Thiamin 20mg
Vitamin A 5,000IU
Vitamin B6 20mg
Vitamin B12 100mcg
Vitamin C 250mg
Vitamin D 1600IU
Vitamin E 100IU
Vitamin K 80mcg
Zinc 15mg