Xenocide is being migrated to a full blown 3D rendering engine named OGRE... Their hardware configuration will be different, alpha 4- were just a concept work, to see what we wanted to do. None of that code is being used now. That is why Alpha 4 is currently very unsupported, you can always download the video
that Micah made to see what we want to accomplish.
I can promise you that we wont have that problems, but I cannot say that we may have similar (those that for the outsiders -non coders- looks the same but they are not), or new ones even if we are trying very hard not to make mistakes...