Here's a simple shape rotation animation. I've enabled the basic layer order animation and the "Project Settings"/ "Eye Separation" is set at .4
For just simply checking a few settings I think AS does pretty good. But,from what I've been able to research on the web (about all that "Horizontal Parallax" stuff)

Also looks like I could use a crash course on "Retinal Rivalry" where the colors are clashing. Also this was rendered using Quicktime/Animation/Best settings. Obviosly the Youtube quality takes a big hit, but even on my PC it's struggling a bit. Rendering with single frames is probably a must.
Maybe future versions of AS could include "Eye Separation" settings in Group Settings. And an Anaglyph Color Safe Swatch.
If anybody else is working on this Anaglyph stuff hit me up if you have advice, online study links etc.