I am confused to if using Rotate() and .rotation will conflict with each other.

I am moving a transform to point at a Target automatically with .rotation and when I choose to move manually I use Rotate(). But after I stop manual control and use the automatic mode the transform will be offset with the manual movement I had done. So the Rotate() is adding offset. The manual control no matter what is accurate. The automatic targeting is added an offset after using the manual control.

Here is the code for the Manual Control.

xDif = Input.GetAxis("Mouse X") * mouseSensitivity.x;
yDif = -Input.GetAxis("Mouse Y") * mouseSensitivity.y;
float zDif = 0; // <-- gets changed with buttons
transformToMove.Rotate(new Vector3(yDif, xDif, zDif));

Here is the code for Automatic Targeting

/// Returns true if the transform has been successfully oriented to fire at the current target.
private bool TrackTarget(out Vector3 hitPosition, out float hitTime)
{
    hitPosition = Vector3.zero;
    hitTime = -1.0f;
    
    if (!IsTargetValid(currentTarget))
    {
        state = TransformState.NoTarget;
        return false;
    }

    if (!GetFiringDirectionToHitTarget(currentTarget, out Vector3 firingDirection, out hitPosition, out hitTime))
    {
        return false;
    }
    
    Quaternion desiredRotation = Quaternion.LookRotation(invertFiringDirection ? -firingDirection : firingDirection);
    Quaternion currentRotation = transformToMove.rotation;
    float maxDeltaAngle = maxRotationDegreesPerSecond * Time.fixedDeltaTime;

transformToMove2.rotation = Quaternion.RotateTowards(
    currentRotation, 
    desiredRotation, 
    maxDeltaAngle
);