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Anybody can have a Roth IRA. Even if you're over the income limit for a Roth, you can still convert a traditional to a Roth IRA after you pay taxes on the amount. These conversions are pretty common and well known.

Says in the article he was below the limit.

If you're reasonably wealthy and you start a firm, there's no problem just taking a smaller salary. It's a little bit surprising that the rules don't address this though. Why not just say Roth IRA is for people with net worth under some figure? Or as mentioned in the article, put a cap on the amount of tax exempt money?

Like every other SV startup, he was paid a decent salary with lots of stock and thus qualified under the income limits.

Probably by a traditional IRA to Roth IRA conversion.