Yep, totally agree with your points.

>What would it even mean for lifestyle choices to directly cause some condition?

The glib answer would be something like woodworking and missing fingers :-)

But there are plenty of people (not me!) who believe, for example, that obesity and type-2 diabetes are directly caused by overeating and/or lack of exercise.

I follow the same logic you do, even though I disagree with what you are saying.

Lifestyle choices increase the risk of these diseases but if they caused the disease, everyone who ate the diet would get the disease, and we know that is not true.

The difference is crucial because we know genetics plays a role as well so matching diet and genetics would be useful.