The segmented mesh and the input mesh are scaled differently.

[mitlislab]

I tried visualizing the segmented mesh and the input mesh, and they seem to have a different scaling and translation. The segmented mesh is larger.

This is the input (penguin) mesh and segmented (penguin) mesh visualized together. Is there a naive transformation to align the meshes together?

[mitlislab]

I also realized that the input mesh and the segmented mesh have the same orientation and are the same mesh (just scaled differently). To adjust their scale and translation, I wrote some simple code which seems to work

mesha = trimesh.load('input_mesh.obj')
meshb = trimesh.load('segmented_mesh.obj')

extent_a = mesha.bounding_box.extents
extent_b = meshb.bounding_box.extents

scale_factors = extent_b / extent_a

meshb_scaled = meshb.copy()
meshb_scaled.apply_scale(1.0/scale_factors)

translation = mesha.centroid - meshb_scaled.centroid
meshb_scaled_translated = meshb_scaled.copy()
meshb_scaled_translated.apply_translation(translation)

trimesh.Scene([mesha, meshb_scaled_translated]).show()

There's perfect alignment now!