Not sure if it’s the same problem/behavior.
When creating my Addon. Produces almost infinite many time-varying geometries with functions I noticed something similar when comparing Geometry and indexed BufferGeometry.
Bottom and top have extra vertices (necessary because of the uv-map). This keeps the edge / seam pretty flat even with smooth.
using .computeVertexNormals()
seam
The normals themselves calculated and then merged.
seamless
I don’t know if you can do that with a model.