As the person who was highly involved in covering TOS-R when it was airing in syndication back in 2006, and the later disc releases, for TrekMovie.com I can tell you that MattM1121 is correct, they actually issued the Xbox Live versions not long after a new TOS-R episode was first aired. The Xbox downloads alternated between 4:3 live action and the 16:9 CG, it was technically a mistake.
Behind the scenes, the CG artists at CBS Digital gave themselves a 16:9 ratio to play in so that they could pick the best portions of the new landscapes/planetscapes to crop to 4:3 for the final airing versions in the US and later on disc (DVD/Blu-ray).
They also did the 16:9 versions for potential syndication in other markets where widescreen TVs had deeper penetration at the time (Japan and parts of Europe). In those markets the live action footage was also cropped to 16:9.
Of course things changed pretty quickly and dramatically from when they started the project in 2006. Streaming is now the norm, and there became no real need to worry about broadcast TV syndication rights, etc.
No shots were removed, the CG shots were cropped to 4:3 to fit with the original aspect ratio.
FYI: Here's the portfolio page for the main CG artist on the project, named Max Gabl, it has the 16:9 versions: