I have no evidence why it should technically be that way either, but I can tell you it's not just a "second or third hand cable select misconception". It is specifically stated that way in all the drive literature that I've read about those 80 pin connectors.

Almost all cables are color-coded to help you remember the difference: the black connector for master, the grey one for slave, and the blue one for the motherboard. Some cables actually have the words "master" printed by the end connector, and "slave" by the middle one.

So there must be some reason why they go to this effort, and given that doesn't take very much effort to arrange your drives such that they can be plugged in this way, I've never really thought to question it. As to whether you don't lose performance the other way, I have no idea, but that would be interesting to know.

John