GJK error in interpolation between non matching second ordered 3D meshes

I use code of @Lingyue_Shen to reproduce the same error, which is self-contained.

It is very similar to my use case, except that he shakes every point in the demo as quoted, whereas I keep the boundary points fixed in application. That does not affect the results.

I gradually increased padding from 1e-11 to 1, and the error persists.