This study is looking at "children aged two to six" (ages at which formula or breast milk would no longer be necessary to sustain life), and the article highlights that non-dairy milks' nutritional content is different from dairy milk, which may have developmental consequences. One possibility is that non-dairy milk meant to consumption by small children should be fortified more (or differently), or that vegan diets for children commonly require more supplementation. I think there's evidence that fortification of dairy milk has had great health benefits, while apparently for particular purposes non-dairy milks are starting out at a disadvantage even if they have some health benefits in other ways.
In the course of my first decade of veganism, I developed significant D and B₁₂ deficiencies which I've recently successfully cured with dietary supplements. I don't think that vegan advocates will do ourselves or our cause any favors by pretending that these deficiencies are rare or difficult to acquire; in fact, they're relatively common and often associated with a vegan diet. (I'm thinking of all the effort that John Robbins spent pointing out that adults can easily get adequate proteins and amino acids from vegetable sources, because this is something people reflexively call into doubt. From what I've heard since, I think he was right on that point, but the same can't be said for B₁₂!) The good news is that these deficiencies also easy to detect and, for many people, they're also easy to cure.
When we're talking about childhood nutrition, the stakes are higher, and it's essential to be better informed and more attentive. A few years of deficiency in these vitamins in my 30s has probably not hurt me for the long run, but it might be a different story if the same thing had happened when I was three or four.