For later stage companies, these are likely in the form of RSUs over options. That makes it a lot closer to giving cash based incentives than stock, especially when compared to owning the company outright from an early stage.
If a CEO owns 60% from the beginning, that's already built into the cap table no matter how big the company gets. If they get RSUs as incentives later on, the company is still footing the bill for giving them an $500 million in stock - an asset the company owned that could have otherwise been converted to cash.
The article doesn't do a great job explaining why giving bonuses later is so much more expensive for the company and its shareholders