I don't understand how this could be the case. If a company pays its employees the prevailing wage, why would it be obligated to pay an H1B hire at the 90%ile?

Either the prevailing wage paid by all companies in the area, or the actual wage paid to comparable employees in that actual company.

Unfortunately, I still don't understand your argument.

If a company currently pays 100K for a senior software engineer, the median for the position is 100K, and the 90%ile for the industy is 180, is the company obligated to pay 180K to an H1B for this role?

My understanding is that it is not, that 100K would meet the prevailing wage requirements.

I'm sorry, I guess I misunderstood your point. No, 100k would work. But if the industry median were 100k and but the company in question paid US workers in that title 150k, they'd have to pay 150k.