As I understand it, it's not that a small population directly causes intelligence loss, but that intelligence is less of a selective advantage in an isolated population

What is required of a successful generation ship to maintain and improve intelligence is to design it in such a way that intelligence remains a selective advantage. The simplest method in the context of speculative future technology would be controlled breeding, but that is not so easily applied to the generation ship that is this planet.

The article argues that small population does directly cause intelligence loss - or rather, that it breaks anything that depend on too many parts of the the genome to be too precisely balanced. But why would you let genetic drift and natural selection operate on a generation ship at all? That's a recipe for disaster; it's nearly impossible to predict what results would come out of it. It'd be much better to bring along frozen embryos (or something equivalent).