The Xbox One runs the original code. "Repackaging for X1 compatibility" basically comes down to simply recompiling the code and adding a config file for the emulator. It also ensures everyone runs the same (latest) version of the game which avoids complications. It's a tad more complicated than that, obviously, but the jist of it is they do not touch the x360 code.
And even then, they could simply add many more games to the BC list if they didn't renegotiate licensing rights to be able to sell the game off the store every time. They could simply make it so your console downloads the BC version of the game if you have the disc, but that BC version isn't available to purchase. Just like if you own driveclub on PS4 you can still download it, but no one can buy it off the store.
The XB1 cannot just run older code nor is it capable of fully emulating the OG/360.
"the team is now at the point now where everything an Xbox 360 can do, its emulator can mirror in software."