Improve the vertex positions in cage topology graphs

[andrewtarzia]

It is more clear in the representations introduced in #495 that some topology graphs, eg cage.M24L48, have imperfect vertex placements.

This issue will likely result in changes to test outcomes because of small building block position changes.

It is necessary to go through all topology graphs.

[andrewtarzia]

An example of a fix:

Update positions of vertex id=3 in stk.cage.M3L6 to:

        stk.cage.LinearVertex(
            id=3,
            position=[
                _R * np.cos((_theta + 1 * np.pi / 3)),
                _R * np.sin((_theta + 1 * np.pi / 3)),
                0.5,
            ],
            use_neighbor_placement=False,
        ),