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Not really. If you think about it, this was made before the RDB standard was accepted, and engineers had no reason to make sure that drives formatted with their software were readable on another's controller. So yes, when they were sending commands to and from the drive, and doing things like finding out (from the drive itself) its parameters, the driver would need to fiddle bits about. As I said, you wouldn't want to do this to yourself without a good reason why, and being able to actually route the traces on your board is a pretty good reason to change something like this. They may have needed to move to a more expensive PCB (bigger or more layers) otherwise.
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