that is a very short sighted assumption.

I'll explain when I'm not on my phone.
EDIT: Explanation.
I don't want to be boastful, but you need to consider my credibility here. While you have read and possibly created some of the code as well as having made or added a few anims to FSO, I have worked with FSO's anims to the limits. I've created over 400 anims (.ani and .eff) and, as far as I know, I've made the only fully functioning 3D mainhalls. I know what I'm talking about.
Now, the first thing that comes to mind is that transparency is a retail used feature with anims. It's also a feature I've used extensively. Think CB Anims.. what if I want a logo anim with a seamless background to match the interface? Best way to do it is to render the animated logo on a transparent background (or full green for .ani). I've also used this for ship/weapon select anims so that they are transferable to any interface style and just just FS2 style.
Now, for mainhalls. You
can not do 3D mainhalls without transparency and have it look good. You just can't. Retail Bastion uses transparency for the cranes, as do I. I also use transparency to blend all the doors and misc anims onto the background seamlessly.
All in all, transparency is an essential thing to be used for a lot of anims throughout FSO. Calling it an art direction issue is extremely short sighted and, frankly, I'm shocked that you, of all people, would say that.