That I think is not practically possible.
If I'm not complete misguided, it is the sata drivers that control what data sent and received from the harddrive.
That is - if it is possible at all, you must be able to provide your own set of sata drivers.
And if that isn't enough - the sata controller is also probably hard coded so it can only communicate in a certain way, meaning controlling the bits directly would be impossible.
Or certainly nothing are impossible. If you can somehow remove the controller chip from the motherboard (advanced soldering methods required) and replace it with your own - which are costly since you have to make someone manufacture it.
And even then - if you're capable of doing that (surely, you then won't be lurking around in these forums anymore, as nsa probably want to hire a guy like you) - there is a fair chance having the controller circuitry embed into the motherboard chipset. You still may be able to trace the pcb route, but it require that the actual conductor is at either bottom or top level - not inbetween pcb layers.