The rationale is that the powers aren't unchecked, but that the check for official constitutionally listed acts of the president is Congress, not the courts.

Article 48 gave the presidentisl office the power to unilaterally bypass the legislature.
This supreme Court ruling delineates the line between the individual and the office with regards to the judicial system, not the relationship between the office and the other branches like article 48 did.
Rather than granting new powers or preventing restraint of the executive branch, it purely limits the consequences the individual can face out of office.
The concept of presidential immunity existed prior to this case.

The ruling essentially listed three categories and their immunity status with regards to the courts. In my opinion, two of them are reasonable and the third shouldn't exist.

It's reasonable to me to say you cannot sue the president for vetoing a bill, or criminally prosecute the president for commanding the military. The constitution says the president can do those things, and that the check on presidential power is congressional acts including impeachment. The office of the president or the government as a whole may be prosecuted, and Congress and the courts can hammer out the exact meaning of the core powers, but the individual is only liable if Congress uses their power to assert that something was definitely not a valid presidential act.

It's reasonable to me to say that being the president doesn't grant you broad immunity for non-president things. The president does not have the constitutional authority to drink and drive, so if they do they're just a person subject to criminal prosecution.

It's unreasonable to me to say that in areas where the president acts officially, but their authority is shared with Congress or an inherent power of the office that they might not have immunity depending on how it impacts the role of the president.
It's weird to say it, but in this case I agree more with Coney Barrett that the more appropriate test is to see if the law applies to the official act and then determine if in this case it would interfere with a delineated core power.

In her own separate concurrence, Justice Amy Coney Barrett agreed with the majority “that the Constitution prohibits Congress from criminalizing a President’s exercise” of his core constitutional powers and “closely related conduct.” But she would have courts approach the question of immunity for other official acts differently, by focusing first on whether the criminal law under which a former president is charged applies to his official acts and, if so, whether prosecuting the former president would interfere with his constitutional authority.

Applying that principle to the facts of this case, she suggested that at least some of the conduct that serves as the basis for the charges against Trump – such as his request that the speaker of the Arizona House of Representatives hold a special session about election fraud claims – would not be immune. “The President,” she concluded, “has no authority over state legislatures or their leadership, so it is hard to see how prosecuting him for crimes committed when dealing with the Arizona House Speaker would unconstitutionally intrude on executive power.”

https://www.scotusblog.com/2024/07/justices-rule-trump-has-some-immunity-from-prosecution/

I ultimately think that it would have been better to say that the president (individual) cannot be criminally prosecuted for exercising specifically enumerated constitutional powers unless Congress has impeached and removed from office and send it back to the lower court. They're perfectly capable of deciding if a particular act was an executive overreach or not on a case by case basis, and the fact that this has never happened before is a pretty solid argument against needing to worry about a "chilling effect" on the exercise of presidential power. The president should be chilled, it's practically in the constitution. Any power not given to the government is reserved to the people, clearly implying that the constitution should be read as stingy with power to the government, and generous with rights to the people. The president, as a member of the government, should be encouraged to worry about wandering around in legal grey areas.