Can BetterDisplay change the image while an XDR reference preset is selected?

Yes. A reference preset defines the display's reference behavior, but separate software dimming and image adjustments can still change the visible result. Applying those adjustments does not rewrite the preset itself.

For work that needs the preset's unmodified output, open Settings > Displays > [display] > Image Adjustments and turn off Enable software-based video adjustments. This disables BetterDisplay's software dimming, color-table effects and overlay/compositor adjustments for that display. It also disables software brightness upscaling and affects combined brightness, which rely on that permission.

This preference leaves the reference preset and any native brightness adjustment allowed by that preset to determine the display's output. It does not calibrate the panel or prove that its measured brightness and white point match a target. If measurements still differ, investigate the selected preset, calibration and display separately rather than assuming a leftover BetterDisplay software adjustment.

See Image Adjustments for the master preference and Presets for reference-mode selection.