On caffeine you are correct I believe the negatives far outweigh the positives for most people. Just as with alcohol or sugar. Yes you can consume these things but most people will have long term side effects from over consumption.
In the USA obesity is a problem. In the USA diabetes is common and metabolic syndrome is a problem. It is known that sugar and caffeine can make those problems worse. So if a person can avoid caffeine, and sugar, and alcohol, then it would probably be beneficial.
Does this mean 100% of everyone has to eliminate that? No. It means people who have the genetics to be concerned about diabetes, or alcoholism, or who are overweight, probably should avoid it.
And we do know that coffee without caffeine is healthier because as I said the component in coffee which is associated with the health benefit has been found. I cited a source to that as well so just isolate that compound and why do you even need caffeine or coffee?