I kinda doubt the new carpet was for TVH - there were never any scenes written for the Enterprise sets in the movie, but for the bridge, even as early as the December, 1985 first draft. The production designer wouldn't have put money into redressing sets that weren't going to be used, simply not cost-effective. That green lighting in the engine core looks to just be a simple lighting effect without the swirling patterns from the vertical intermix chamber - it might've always looked that way, we just never saw the horizontal core lit by itself on screen.Actually the corridors were given a royal red carpet for their TVH/Enterprise-A appearance. And the intermix chamber was given new green lighting. These can be seen on the Good Morning America set tour.
EDIT: here's some shots of the Enterprise corridor from Roddenberry's intro for The Cage. As you can see, there are no carpets anywhere to be seen. I'm thinking those red carpets were put in for the set tour to minimize the sound of footfalls so they wouldn't have to go back and ADR the video piece.
http://tos.trekcore.com/gallery/albums/0x01/thecgaeintro01_004.jpg
http://tos.trekcore.com/gallery/albums/0x01/thecgaeintro01_005.jpg
http://tos.trekcore.com/gallery/albums/0x01/thecgaeintro01_017.jpg
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