Hello Mina,
DEM-based volume measurement calculates the volume in the selected extents defined by shape above/below the specified level. For your case Best fit plane may be optimal, I assume.
But if you are using mean level option applying it to the model oriented differently it of course will give you different values, because the cut off plane is different, since you are changing coordinate system axis orientation.
Note that custom level value in 1.3.0 build 3772 is working incorrectly, unless called form Python API.
Just a rough illustration of what I'm speaking about: