Note: I'm not on the development team; I'm just the contact in the Raspberry Pi Foundation. I didn't choose the coordinate system - I assumed it was the same as in the Pocket Edition.
Documentation will be released when they/we have decided what the interface will be! As an example, though, the current setblock is implemented by sending "set-block(x,y,z,type)\n" as plain text. When I make large edits (> 10000 blocks), it takes a while for the world to update, so I might suggest having something more efficient too.
The game isn't a shared object file on the Raspberry Pi - it's just a normal executable. Would your proposals still work? If so I'll look into it when I have time; probably next week.