Scaling down a mesh flattens the object

[inmim]

Afternoon all,
I've been working this problem for 2 days now and not understanding the "why" it is happening.
Background: have a small object 3d model, looks great at a normal scale. The axes limits are x +/- 2, y +/- 2, y +/-4 with x at latitude, y as longitude, z as depth. 3d mesh is imported, rotated x 90deg. BUT lat/long moves are small in the 0.001 incremental range so it never looks like the model moves in the 3d graph. So, I want the plot scaling to be 0.002, 0.002, 4 (where lat/long = x/y, and depth is normal units

I've tried using the trimesh methods to rotate (works... found that out after I made my own rotate functions) and scale (works with 2,2,4 but not 0.002)
I've made my own scale function and it works as well

Is it a matter that 0.002 is too small a factor?

`
# 2,2,4 works, but need better fidelity of lat/long so need 0.002
#static.scale_factor = [2., 2., 4.]
static.scale_factor = [0.002, 0.002, 4.]

    #loading the mesh, then scale and transform scale the Y as it is rotated 90 deg, rotation after
    static.mesh = trimesh.load_mesh(path_mr)
    static.mesh.apply_scale((static.scale_factor[0], static.scale_factor[2], static.scale_factor[1]))
    static.vtx = [implot3d.Point(v[0], v[1], v[2]) for v in static.mr_mesh.vertices] 
    # this is another way to scale that works w/2,2,4 but not 0.002
    #static.vtx = [implot3d.Point(v[0] * static.scale_factor[0], v[1] * static.scale_factor[2], v[2] * static.scale_factor[1]) for v in static.mesh.vertices] 
    static.vtx = rotate_pitch(static.vtx, 90) # current manta ray model is rotated 90
    static.idx = static.mesh.faces.flatten().tolist()
    static.mesh = implot3d.Mesh(static.vtx, static.idx)

    ...

 # the start of begin_plot
 if implot3d.begin_plot("##Mesh Plots", flags=plot_flags):
    # Setup axis labels
    implot3d.setup_axes("Lat", "Long", "Depth")

    if static.change:
        static.vtx = change_position(static.vtx, static.point)
        static.mesh = implot3d.Mesh(static.vtx, static.idx)
        static.change = False
        implot3d.setup_axes_limits( static.point.x_lat - static.scale_factor[0], static.point.x_lat + static.scale_factor[0],
                                    static.point.y_long - static.scale_factor[1], static.point.y_long + static.scale_factor[1],
                                    static.depth - static.scale_factor[2], static.depth + static.scale_factor[2],
                                    implot3d.Cond_.always)  

def rotate_pitch(vertices, theta):
    angle = math.radians(theta)
    c, s = np.cos(angle), np.sin(angle)
    rotation_matrix = np.array([
        [1, 0, 0],
        [0, c, -s],
        [0, s, c]
    ])
    # Apply rotation to each vertex
    return [implot3d.Point(*(np.array([v.x, v.y, v.z]) @ rotation_matrix)) for v in vertices]

def change_scale(vertices, amount: list):
    return [implot3d.Point(*(np.array([v.x * amount[0], v.y * amount[1], v.z * amount[2]]))) for v in vertices]

`