Ah, that. Annoying limitation yes and I thought I could have better news but not. I thought that if we had a 3D custom symbol, then we could use it in 3D. Slow but workable. But not. Custom symbols seem to be 2D only.
# Create a low res sphere (not documented yet)(
FV = GMT.geosphere(2);
# Create a EPS file that will be used as a custom symbol (it HAS to be an EPS)
plot3(FV, frame=:none, name="sph.eps", show=true)
Getting better, but still complicated by the often axes non-isometry and since these symbols have map instead of paper coordinates. Also, potential slow when the 3D symbols are complex and have many triangles.