First, sets have always changed between movies. Second, they can't go in the brewery again and rebuild the thing precisely like they did it last time. Third, it looked pathetic, precisely like a brewery. Fourth, they have a bunch of decent, not great but decent sketches for engineering sitting on their shelves. Fifth, it hasn't been necessary to focus on central engineering because Scotty has been absent for a large part of the movie.
Five reasons to design a new engineering set. I'd bet a thousand bucks to a hundred that the Budweiser sets will not be seen again. Doesn't mean that the product placement, another disregard of the general principles of Trek, will stop though.