>and therefore the only real differences that can remain are the genetic differences.

Incidence of undiagnosed digestive and sleep disorders, like celiac disease and sleep apnea, respectively. "Catch-up" growth occurs almost universally after treatment starts, which means that the growth trajectory was lower than the "genetic potential", and likely remains so for children who can't access treatment.

Multiply across any number of silent or untreated disorders, sensitivities, or insufficiencies.

Adult height also isn't 90% heritable in the US. It only reaches that high a percentage of heritability in studies involving closely-related populations. In which case, of course; in populations with low genetic and cultural diversity and moderate or high variability, small differences are magnified.