Or does it?

They may have raw intelligence, but poor thinking habits—patterns of absorbing, processing, and filing information. Cognitively, they aren’t set up to get to the heart of a matter, to distinguish between essential and accidental details, to form and apply valid generalizations. This too may require patience. It isn’t good, but it isn’t willful, irrational, or stupid. Concentrate on what other virtues and talents they bring to the table, such as creativity, diligence, or relationship-building.

This seems to mean exactly "maybe they are stupid after all", but expressed using a different set of words.

(I would guess that the author at some point adopted "never think that someone is stupid" as a deontological rule, and then unintentionally evolved a different set of words to be able to think about stupidity without triggering the filter...)

You're right. I'm sure that actual stupidity is sometimes the real problem. On the other hand, it would surprise me if it's always the real problem. At that point, the question becomes how much effort is worth putting in.

I think purely from a fundamental attribution error point of view we should expect the average "stupid" person we encounter to be less stupid than they seem.

(which is not to say stupidity doesn't exist of course, just that we might tend to overestimate its prevalence)

I guess the other question would be, are there any biases that might lead us to underestimate someone's stupidity? Illusion of transparency, perhaps, or the halo effect? I still think we're on net biased against thinking other people are as smart as us.