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...)