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The so-called 30-day amendments to the governor’s annual budget proposal are a little like the ugly stepchild of state government.

While Gov. Andrew M. Cuomo uses the State of the State address and his budget speech to showcase new, flashy policy ideas (Green New Deal! Legalizing marijuana!), his budget amendments get none of that. There isn’t even a news conference. Instead, the amendments — a series of fixes and tweaks issued a month after the proposal — arrive, largely unheralded, in a packet of dense legalese posted to the governor’s website.

But the amendments’ low profile belies their importance. They can move up or push back a program’s start date; add or eliminate large sums of state spending; even, in some cases, throw in new ideas entirely, without lawmakers’ or the public’s notice.

Blowing up the M.T.A.

Mr. Cuomo has been on a rampage to “blow up” the Metropolitan Transportation Authority, which controls the city’s flailing subways and commuter trains. Without an overhaul, the governor said, the agency would continue to stew in its own bureaucracy and lack of accountability. (The M.T.A., a state agency, is controlled by Mr. Cuomo.)

The updated budget provides the first hints of what that blowup would look like.

M.T.A. board members would be forced to step down when the elected official who appointed them leaves office. The agency would be required to come up with a “comprehensive reorganization plan.” The governor would also add a layer of bureaucracy by creating an “expert panel” to oversee and approve the M.T.A.’s spending.

“We have to consolidate the functions at the M.T.A.,” Mr. Cuomo said in a recent radio interview. “Bring in a different culture. Make the board functional and operational.”

The panel would also be in charge of structuring a much-debated congestion pricing plan, which would raise money for mass transit by charging people who drive into parts of Manhattan.

The bill states that the panel can issue the congestion pricing rates “no sooner than Nov. 15, 2020” — even though Mr. Cuomo has called on lawmakers to pass congestion pricing this year. Mayor Bill de Blasio joined that call for the first time last week.

The restructuring plan could give Mr. Cuomo (even more) significant control over the M.T.A., after years of him denying or downplaying that influence. The governor suggested in the radio interview that he would ask legislators to consider changing how the agency’s board members — of whom Mr. Cuomo controls a plurality but not a majority — are chosen.

Some lawmakers have already expressed skepticism. State Senator Liz Krueger, a Manhattan Democrat, said the scope and purpose of the expert panel, as well as the governor’s long-term plans for the M.T.A., remained unclear.

“There are many still unanswered questions, and numbers that don’t necessarily add up right,” she said. “But I certainly agree that we have a crisis for mass transit funding, and dramatic solutions must be implemented.”

Buckling up

What do seatbelts have to do with state spending? Unclear. But they’re in the budget anyway, in the form of a proposal to make back-seat passengers wear them.

Currently, it’s illegal in New York to ride without a seatbelt in the front seat, and in both the front and back for anyone under 16.

It’s not contested that rear seatbelts save lives: A 2007 study found that crash mortality could be reduced by as much as 75 percent for people in the back seat if they wore seatbelts.

But that doesn’t explain why the proposal was in the budget, rather than introduced as a separate bill. Except that this is how the budget in Albany is always done: crammed with nonfiscal matters that the governor or other lawmakers want. After all, it’s harder to reject any one policy when it’s tied to a $170 billion budget for the entire state. Ah, transparency.

Prison closures

One of the perhaps most unexpected amendments was Mr. Cuomo’s proposal to close up to three prisons by September, an idea he had made no mention of in earlier speeches.

The governor celebrated the idea as a common-sense step toward criminal justice reform, especially given the state’s declining prison population. The state Department of Corrections and Community Supervision would decide which prisons to close, and the closures would not cause layoffs, Mr. Cuomo said in a news release.

But Republican lawmakers and corrections officers accused the governor of trying to sneak the closures under their noses, endangering public safety.

“Closures do not in any way equate to a decrease in number of incarcerated people,” said Michael Powers, the president of the state’s correctional officers union. “Closures mean consolidating the same number of incarcerated people into a smaller area, making remaining prisons overpopulated.”

Still, the proposed closures are likely to be among the least contentious criminal justice issues before the Legislature in coming weeks. Democrats in both the Senate and Assembly have promised to reduce or even end cash bail, ensure speedy trials and guarantee defendants’ access to evidence — measures that divide not just along partisan lines, but even cause disagreement among Democrats.

Cuts to hospitals

Talk about whiplash. First, Mr. Cuomo’s budget promised a 2 percent bump to Medicaid reimbursement rates, much to the joy of hospitals and other health care providers.

Then, the reversal came: The amended budget cut reimbursement rates, after Mr. Cuomo announced in February that the state was facing an unexpected $2 billion shortfall.

The new budget would reduce state funding to hospitals by more than $500 million — a gross loss of more than $1 billion after the loss in federal matching funds, according to Bea Grause, president of the Healthcare Association of New York State.

If passed as proposed, the budget would make the biggest cuts to health care spending since Mr. Cuomo took office. But Ms. Grause said she was confident her group could talk the cuts down.

“It’s the opening play in a larger negotiation,” she said.

A fee on opioids

If this sounds somewhat familiar, that’s because it is. Mr. Cuomo last year signed a law requiring opioid manufacturers and distributors to pay into a $100 million annual fund, which would be used to pay for substance abuse treatment programs.

But in December, a state judge shot that down, ruling that the law as written would obstruct interstate commerce.

So this year, Mr. Cuomo is trying again. This time, he is structuring the fee as a tax rather than a fund, and more important, explicitly allowing manufacturers to pass the cost on to patients — a provision that last year’s law prohibited.

That has raised concerns about hurting people who genuinely need the medication. “The proposed tax is effectively a tax on pain,” said Lewis Davis, an economics professor at Union College who studied the proposal at the request of a group of pharmaceutical research companies.

But Senator Peter Harckham, the Democratic chairman of the Senate’s Committee on Alcoholism and Substance Abuse, said he supported the change as a necessary concession to the goal of fighting the opioid epidemic.

“Unfortunately it’s the way that the courts will allow it,” he said.

The Legislature would study possible exceptions for some patients, he added. “But if this is an impetus to change the conversation from opioids to other medications that are not as dangerous, then let’s use it as such."

Vivian Wang is a reporter for the Metro Desk, covering New York State politics in Albany. She was raised in Chicago and graduated from Yale University. @vwang3

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