The flickering on the surface of your spin movie is a limitation of the ChimeraX ambient shadow calculation. When you spin each model about its own center then the shadows have to be recalculated every frame because models are moving relatively to one another and so different shadows are cast. The ambient shadows are cast from 64 different directions (not very many) and that causes flickering on the surface. When you rotate all models at once in ChimeraX then in fact none of the models move in the scene coordinates and the camera simply rotates around the models and ambient shadows are not recomputed, so you don't see any flicker.

The ambient shadows are from uniformly distributed lights in the scene coordinate space. So to reduce the flicker you increase the number of ambient shadow lights. This will make it render much slower. Using the default 64 shadow directions does 64 renderings to compute the cast shadows. So using 512 shadow directions will be 8 times slower. And there is a limit to how many directions your GPU can handle due to a graphics language buffer size limit. At any rate you can ask for 512 shadows using

In addition to the number of shadow directions there is a shadow map size that is the size of the 2D texture that records the shadow depth for each light source. By default ChimeraX uses 1024 x 1024 which is shared by all the lights. If you increase that number the shadow boundaries become sharper, decrease it and they become blockier. Both directions give artifacts and the value more controls the extent of the artifacts, larger spatial scales for smaller texture size, finer spatial scale artifacts for larger texture size. In tests I found 1024 light directions with 4096 texture size was noticeably better than 512 shadow directions and 4096 texture size.

Here I attach a spin movie with the standard settings 64 light directions, 1024 shadow map size (took ~5 seconds to record), and following that a movie with 1024 light directions and 4096 shadow map size (took about 3 minutes to record).