The report seems to have cash salary only.

Most of these companies have a significant payout in stocks every year, and the ratio of stock to cash gets bigger the higher you go in the company.

I can confirm for the amazon amount(under level IV) is not cash only. That's total comp.

Employment in software engineering is very bottom-heavy everywhere.

The number of software engineers doubles every five years. That means half of all software engineers have less than five years of experience. (And 75% have less than ten years, and 87.5% have less than 15 years, and so on.)

Medians seem to be in their self reported dataset, which surely isn’t a representative sample.

I think it lists the Top 10 companies, and then latter on lists the median salary across all the companies they have data for.

Ah, that makes more sense. Different data sets for each list.