Also, if memory serves, all the Enterprise footage was shot by Trumbull and the Klingon ships and V'Ger were all shot by Apogee/Dykstra...
I believe that's correct. However, I believe the actual V'Ger cloud was done by Trumbull, while the V'Ger model itself was shot by Dykstra.
As for the choice of blue screen vs. black background, I don't know why ILM would have chosen one over the other. But, regardless, I still think it is a shame that they had to ruin the beautiful paint job to accommodate their chosen method of filming.
Trumbull's TMP spaceship shots are accomplished via the techniques developed for Close Encounters and later improved upon for Blade Runner. The models are photographed against black velvet because then you can light the model any way you want as opposed to lighting to prevent blue-screen spill and other issues. But since the models can have black in them, then you have the problem that you can't pull a luminance matte off the photography because anything black on the model will be see-through. So, what you do is replace the black velvet with a backlit white screen and repeat the camera pass to shoot a high-contrast black and white image, where the ship is a dark silhouette against white. Push the contrast in post and you get a pretty solid matte element (albeit reflections are sometimes still a problem, so you might have to have artists hand animate fixes). This is known as Hi-Con matting. In some productions, they wrapped the models in white (maybe gauze) and shot a second pass against black to pull a matte that would have no reflections.
The problem is that ILM didn't do hi-con mattes. Their system at the time leaned heavily on the photochemical blue-screen process, where you shoot different passes of the model against a solid blue background. In the lab you do some tricks and the blue doesn't print and ends up as clear, so that's how you get the mattes. Now, the Trek features after TMP were lowish budget, so for ILM to do the shots economically they probably had to do what they could to shoot and process the shots with a miminum of fuss. A pearlescent model is doomed to a lot of blue-screen spill, so their apparent solution was to dull down the paintjob. I'm not certain precisely when this happened, as some of the Enterprise shots (notably the initial approach to the Reliant) still appear to have some of that pearlescence, but it's possible that as the production progressed that dulled the model more to make it easier for them to photograph.
Hope that makes sense.