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The missing line from the summarizing lead:
The increases in average height are closely linked to rising childhood obesity among poorer children and widening socioeconomic inequalities.
So the reasons are child poverty and the accompanying unhealthy diet.
Cool, how does obesity cause tallness though?
Body-fat caused hormonal imbalances (mentioned in the article).
This also includes estrogen and testosterone, linking it to precocious (early) puberty.
And it doesn't exactly cause tallness, but often quite the opposite (as you already mentioned): Affected persons typically are shorter than the norm once grown up.
It just triggers growth at an earlier point in life, so the children are taller on average at a certain fixed age.
It's right there in the article, first paragraph:
Being overweight or obese causes hormonal changes, which accelerate children’s development. Obese children grow faster, so they tend to be taller than their healthy-weight peers. But obese children have a greater risk of disease in later life, including diabetes and heart disease.
Without further research on my end what this means to me is "poor children are more likely to be obese and reach their, presumably shorter, adult height earlier in their childhood".