I'm still not entirely sure I understand the licensing issue that prevents MS from just doing it. If the game is available to download on XBL for 360, what's the difference?
Is it that the code has to be modified/appended that requires the permission?
Technically it is because a new copy is being created. Only the copyright owner can give that permission. It is no different than say, a new run of discs being printed, from that perspective.
Microsoft had two major options when implementing Xbox 360 BC on the Xbox One.
1) Create a single VM, read games off disc, allow emulator access to all system hardware.
2) Create a single VM, but package it with each individual game. Limit hardware access, and package each game with a full set of title art and information.
MS opted for option two.
Going the first route wouldn't have required publisher permission, however it would have opened potential security holes and whenever someone played a 360 game on the XBO it would just have shown "360 game" as the title. Same would be true for disc art, screen shot and video captures, there would be no game hubs, no tiles in your collection, etc.
By going for the second route there is a duplication of emulator data and distribution permission needs to be obtained, however each individual game is treated as a separate entity by the XBO. All features that apply to a XBO game apply to a 360 BC game running on the system. And because the emulator has very limited hardware access there are less potential avenues for exploits. Even the game disc isn't directly read. It is simply used as a license key.
It's being played on a different console with emulation, the user agreement when you buy a 360 game (any game) does not allow that.
Permission isn't needed because it is running on an emulated system. Permission is needed because a new copy is being made. This is also true of XBLA titles because a new system license is being created, which means another licensed copy.