It's not that huge a task, really, but the required equipment is somewhat exotic.
You need to identify the CPU being used in the MD unit, and decode its firmware. You need to be able to rewrite the firmware. This was already hard enough in the MDH10 data drive because the thing used 3.3V parts instead of typical 5V parts. I'd guess that modern units are using 2V logic now, who knows. It's easy to find a cheap EPROM programmer that works with 5V logic, much more expensive to find something that works with all the newest low voltage parts. Sony may have built their own custom microcontroller for these newest units, so it may not be an off the shelf chip with readily accessible documentation. So that may be a real block.
Not having seen a service manual for any NetMD units, I have no idea what chips are used inside...
But until you rewrite the firmware to allow uploads, none of the other stuff (USB protocol, OpenMG shit, drivers) means anything. The firmware has to be fixed to allow the access first.
As for the audio encoding - for LP mode that's already a solved problem. Software to encode/decode ATRAC3 is already freely available all over the web. There's still no free ATRAC1 codec anywhere, but it wouldn't take much effort for a dedicated programmer to make the ATRAC3 codec handle ATRAC1.
OpenMG checkins don't actually transfer the music back to the computer. All it does is check the track info - title, date, etc. The music doesn't move.