I have similar issue.
I'm using the legacy MLSDK default configurations:
Under the XR Rig game object the session origin tracking mode origin set to Device
In the Main Camera game object, Recenter XR Origin At Start is disabled
I configure the inputSubsystem tracking origin mode to unbound and called to TryRecenter as defined in the Unity (OpenXR) MLCamera documentations (link)
But when I call to MLCVCamera.GetFramePose(extras.VCamTimestamp, out var outTransform) I get the transformation between the frame and the origin where the magic leap powered up and not where my application started.
I tried to set the subsystem tracking mode to Device, but the outTransform was the same.
Sorry for the late reply, I noticed the post was categorized in the wrong place.
It sounds like you are having issues aligning the Unity Origin and the MLCamera API? Or are you using the B&W World Cameras?
You mention that you are using the MLSDK configuration. Is Magic Leap XR selected under the XR-plugin Manager Settings or is the OpenXR option selected?
You might be running into an issue that is a limitation of how input is handled inside the Unity Input System and the XR Plugins. As a workaround, you could parent your scene objects to a "root" transform. Then simply move the transform and all of it's children to the current camera position as a way to "recenter". This would visually have the same result as resetting the Unity Origin via the input system.