I'm not quite sure what your asking so this answer might not be what your looking for...
The data encoding is handled by the hard drive controller in the hard drive itself. It will be set up to read whatever protocol, MFM or RLL or PRML etc, they write. Otherwise the drive would be completely useless. Therefore there would be no need for any mapping in the controller as it will only use 1 protocol.
All data read and write requests to the hard disk are sent via the appropriate bus. IDE or ATA etc. These requests are read and interpeted by the hard disk controller, which then performs the necessary actions with the drive mechanism to either write the incoming data or read and output the read data. This means that the CPU, and hence the OS, never needs to know what protocol is used on the hard disk platters and just needs to know how to talk to the appropriate data bus.
Is it just me, or does something smell suspicious about all this?