Note that schools may/may not choose to participate, and the same with students.

They control for schools opting not to participate; see the section under substitute schools.

It's standard research ethics that minors (and their guardians) be given the option to refuse to participate in a study.

Also, homeschoolers, one of the strongest demographics for ethnic and intact family reasons, are likely missed by this sample, skewing results in the US down. They appear to be about 4% of the total population, disproportionately white and in two parent households.

Now I'm confused. The original inference Sailer drew from PISA was that American students outperform their racial group in other countries. You're claiming the study will be biased against white Americans. If anything you should be annoyed at Sailer for trying to support his racial performance narrative using a study that didn't really focus on it.

Regarding homeschooling in particular, it'd be nearly impossible to develop an international study on the same scale of PISA (which you already want to reject as too small) merely because homeschooling isn't prevalent in most of the PISA-participating countries.