Yeah, it's a bit funny that they are ok with declaring some of the matte shots not up to HD standards but won't do that for any of the model shots.
While I tend agree about the 2-footer being pretty sad and detracts from most of the shots it's in, ship shots are not exactly comparable to matte paintings.
The matte paintings are basically just static paintings, they usually aren't recomposited into a shot, they were already part of the set dressing or they are their own live shot without any actor in it (like an establishing shot of a cityscape). And they certainly aren't like the various passes of the models which have a lot of ability to be tweaked and re-lit when composited into a scene, all the while still technically using the original footage (as evidenced by the differences between HTV and CBS-D's handling of the model footage).
With a matte painting either there is plenty of detail that looks good in HD or their isn't. If you look at the special features of Season 2, they have shots of the original Borg cube matte painting. It is a beautiful painting, but it was clearly done with limits of standard definition TV in mind. The brush strokes become quite obvious in HD when the camera gets closer to the matte painting.
Another case where they may enhance or change things is if it's a re-used matte painting. In the case of re-uses, like TOS-R before it, they have decided to allow for some artistic license to tweak the matte paintings to keep it from being a complete repetition.