Can I turn native automatic brightness on or off from the command line?

Yes. BetterDisplay exposes the native automatic-brightness setting through its CLI for a connected display that supports it. For example:

betterdisplaycli set -name="Built-in Display" -autoBrightness=off
betterdisplaycli get -name="Built-in Display" -autoBrightness

Replace the display name with the intended display’s name. Use on instead of off to enable automatic brightness. BetterDisplay must be running with CLI access enabled. See CLI examples.

This changes native ambient-light-based brightness, not the separate synchronization rules for an external monitor. The display must expose native auto brightness, and Enable native auto brightness management must be enabled in Settings > Displays > [display] > Device Control > Device Control Settings…. If you disabled that option to stop BetterDisplay managing the setting, use macOS System Settings instead or deliberately re-enable management first.

Use the explicit command rather than editing an undocumented macOS preferences file. A successful command does not prevent another app, system action or automation from changing the setting later. See native auto brightness management and external brightness synchronization.