Yes those "rows of boxes" are escape pods. I didn't really notice any problems with the "CGI Enterprise" (assuming it was one) in any shots. But I suspect that as the project goes on the final versions will be more perfected. To put it bluntly, this sampler disc is probably very much a "rushed job" to give the idea of what they are doing.
Another thing that I noticed with the ship in that shot was that it was very white. When they showed the ship in the opening credits and later on, you could see the blues and greens that had been used to make the ship appear the gray that it was, plus the lighting made the ship look lit up, but grey at the same time, and made it look real, not a plastic toy.
But with the escape pods, when you look at the shots of the D in the oc's and later in the episode, you'll notice that the escape pods actually stand out away from the ship, whereas on the CGI version they are flat into the hull and look like someone just took like a paper clip and scratched the "boxes" into a piece of plastic.
But with the CGI models, you also have to remember that when TOS-R was put into production, the models for Balance Of Terror & Miri
and those early TOS-R episodes looked a hundred times better than the CGI D in Inner Light
, and they were rushed jobs too. But those models I still remember when I saw my first episode of TOS-R, I thought were long-lost frames of film that had been shot in the 60's with the physical models, and they didn't look anywhere near the low level of CGI that Eden FX used for Enterprise. So, hopefully CBS Digital will get the CGI up to a higher level.