The distances between sockets on the cord are designed to minimise data corruption and signal propogation problems.
As for it working no matter which way round things go, you're correct, that's because the cables are literally straight end-to-end affairs which as long as they're inserted the right way up on each device, and as long as none of the devices is set to 'cable select', will work.
However as a guideline, you'll get the best performance out of the shortest possible cable, hooked up the recommended way, from the supplier which uses the highest quality materials. Good luck on figuring that out
better cable means less data re-requests due to interference on the cable, which all happens transparently, and we're talking milliseconds each time, I think.
One other issue is if you hook the master up on the middle cable socket, and leave the end socket hanging free, the signal has more trouble between the motherboard and the drive, because of the drain of this free cable length.
More info here:
http://www.ata-atapi.com/
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