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Hey, it looks like for that mesh the mesh.face_adjacency_projections, or the distance above or below a the plane of a neighboring face's single unshared vertex, aren't all "behind" the face which is what mesh.is_convex is checking:
Looking at the mesh with the "bad" faces shaded red it kind of looks like that modifier might be taking the convex hull of some "potato chip" quads, and then the triangulation is done after the hull resulting in a non-convex triangular output? Here's the notebook I was playing with.
When running blender's Convex Hull operator on a suzanne mesh, the produced mesh does not pass the is_convex check provided by trimesh.
Model:
convexsuzanne.zip
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