I think the comic is just talking about how the Enterprise-A doesn't look much like the Enterprise NX-01. It doesn't say the NX-01 was IN the movie. I'm not sure what people expected the NX-01 to look like, honestly. It looks perfect to me; what do they need, to see the strings holding it up or something?
I mean seriously, it's 2004, and production design is through the roof these days, especially when compared to the original series in the 60's. I don't think anybody would want to see a ship that looks "worse" than the original Enterprise.
Think about it, designing the NX-01 for the show had to be very difficult. How do you make a prequel to a show that came out in the 60's, when the special effects were so sub-standard, and still stay "true" to the series? To me, the NX-01 looks about perfect, and I think they did a wonderful job designing it.