Eating a diet largely of white rice directly causes beriberi. At least 9/10 people will get beriberi if they eat a diet that's mostly white rice. The median human body needs a certain amount of thiamine to operate properly, and without that certain body functions will cease to occur properly.

Eating too much spinach will cause kidney stones, but by exacerbating a different underlying cause (not directly). 9/10 people will not get kidney stones by eating too much spinach. Making the lifestyle choice to eat smaller amounts of spinach than the general population will protect against kidney stones, but it doesn't mean that spinach is bad to eat.

Without knowing the difference in bodily makeup that allows spinach to influence the occurrence of kidney stones, doctors will vilify spinach. But once the bodily factor that causes this will known, they'll either be able to treat that or recommend lifestyle (diet) changes specifically to the people who have that mutation, rather than vilifying spinach in general.

>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.