The author seems pretty confused.

Effective altruism’s picture is one in which single individuals, with independently formed utility functions, choose between different options in ways that maximize their utility.

Effective altruism is not a moral theory, so it's not the same thing as utilitarianism, and it does not make an assumption of following standard microeconomic choice theory. What it does assume is that the money and luxuries owned by a typical Westerner with disposable income can be put to better use providing things like health support services or cash transfers to the underprivileged in the developing world. That doesn't require robust consumer choice theory, it just requires common sense. (That being said, standard microeconomic choice theory where individuals have behavioral utility functions and choose from different options in ways that fulfill their preferences, actually is very plausible, and less controversial than utilitarianism.)

There is something deeply consumerist about it: you pick effective ways of spending your money just as you would pick the best value-for-money-deal from a restaurant menu.

Well, you could interpret it that way. Or you could interpret it as something deeply legislative where decisions are made based on finding the right way to benefit society. Or you could interpret it as something strikingly akin to military decision-making process where you select the best course of action within your operational constraints. Or you could interpret it as very similar to religious tithing because you have a duty to give away some of your income. You can go on and on with these comparisons, but none of them really mean anything.

I take it that there is something missing in this picture, something deep and important about human life.

This seems to be the heart of what the author is trying to say, but ultimately it misses the point. Effective altruism is not a moral theory and it doesn't aim to provide a complete picture of why human life is important or what the ideal world would look like; if that's what you were looking for, then effective altruism is the wrong place. It is a moderately constrained set of questions about how to apply one's time and money to solving the most pressing global problems. Conceptions of the human life do not contradict and are not precluded by effective altruism.

There is a strand of philosophical thinking, from Aristotle to Hegel to Marx, that provides an answer, and this answer fits much better with the best evidence about human nature that we have from history and from psychological research. According to this picture, human beings are social and political animals. They live in social structures that they inherit from the past. Non-cognitive elements play an important role in maintaining them. They are undergirded by institutions, including those that regulate access to property rights and to control rights.

The author seems to misunderstand the microeconomic choice theory which effective altruists don't even assume to be the case - in microeconomics we don't ignore subtle social and political influences on individuals, either it's something that is a given influence on their final behavioral utility function, or it's in the domain of behavioral economics.

What matters for a good human life, in which basic needs can be justified and individuals have some degree of autonomy, is that these institutions and practices function to the advantage of everyone.

Absollutely.