On macOS Sequoia, running the sudo spctl –global-disable command to disable Gatekeeper produces the following output: Globally disabling the assessment system needs to be confirmed in System Settings.
There seems to be an intentional change in Sequoia, focusing on security through preventing automation.
Jeff Johnson encountered issues when trying to disable System Integrity Protection (SIP) using the csrutil disable command in Terminal on the recovery volume. He received an error message related to the firmware change caused by Sequoia that prevents csrutil from working with previous macOS versions.
In previous versions, Sequoia made changes such as removing Gatekeeper Contextual Menu Override in macOS 15.