It's right there in the article:
Rather than negotiate against Musk with the mindset of a third party, the Compensation Committee worked alongside him, almost as an advisory body.
In a public company, the board has to negotiate with the CEO as if they are competitively hiring a salaried employee to manage the business. The expected pay could be estimated as follows:
CEO compensation usually depends on revenue and income metrics. It ranges between 0.01% of total revenue and 1% of net income. For instance, Apple's CEO Tim Cook earns ~$100 million, while the company brought $100 billion in net profit in 2022 and 2023. That is 0.1%, high-end pay for a high-performing CEO.
Tesla's revenue in 2018 was $21 billion; in 2023, it reached a revenue of $96 billion and net income of $15 billion. On the open market, this would typically result in CEO pay between $10 million (0.01% of revenue) and $200 million (1.3% of net income).
Stock growth is already accounted for in CEO pay by making it mostly stock options.
The agreement reached in 2018 provided an unusually large stock grant, tied to share price increases. This ended in a total compensation package of $56 billion - 300% of the company's net income. It's stock, not cash, but it effectively reclaims 10% of the company for Elon.
Nominally, the board is supposed to negotiate for the lowest reasonable pay package for their choice of CEO to take the position. The judge didn't believe it was the best possible price in Tesla's case.
“Swept up by the rhetoric of ‘all upside,’ or perhaps starry-eyed by Musk’s superstar appeal, the board never asked the $55.8 billion question: Was the plan even necessary for Tesla to retain Musk and achieve its goals?”
The court found that the board was essentially negotiating the best deal for Elon, which the shareholders weren't aware of. It also didn't find such compensation consistent with what an independent board of directors would reasonably negotiate with an independent CEO-for-hire.
Effectively, both sides took a gamble, and hit a jackpot. Musk has the right to gamble in this manner, but a public corporation's board, according to this particular court ruling, is not.
This is the legal reasoning. The underlying reason could be that CEOs are a frequent target of criticism for wage disparity. The aim could have been to avoid a new upward spiral in wage ratios. This package would've been the first time it crossed 1,000,000:1.
Elon Musk may be an exceptional talent, but it always starts with the exceptions. In 10 years, it could be Calhoun (man who sacrificed Boeing's reputation for quality to drive up stock) negotiating a similar package. Short-term, the shareholders gain, but it's not necessarily in the nation's long-term interest. Delaware is a very pro-business state, chosen by most US corporations, but also a blue one, which tend to prefer less income disparity.
Regardless, that's speculation, and the official reason is that the board didn't negotiate in good faith to reduce it to a reasonable minimum at which Elon Musk would have accepted the job.