I agree with this criticism in the case of sleep apnoea, since the respiratory system is complicated. By intuition, it seems like the evolution of a complicated trait should require significant genetic changes, and thus be more likely to get stuck in a local maximum. I'd expect the respiratory system to be quite resistant to change: what if you've got an SNP that reduces sleep aponea but also prevents peristalsis, speech, weakens your neck, etc.? You might need a number of SNPs to all change at once in order to fix the problem.

I don't think the argument holds so strongly for questions like "why don't we produce GLP-1 hormone at a 20% higher level?" Increasing GLP-1 production levels seem like a smoother transition with fewer side effects. If higher production is better, and you've got an SNP that increases production by 5% on its own by increasing the number of L cells in your intestines (or something), that sounds like it should make you more reproductively viable in today's world and shouldn't have as high an impact on everything else as changing the shape of a throat.

Most of this is just my intuition, and I'm absolutely not an expert.