Since they have transparent aluminum, that means they adjust the color on the molecular level, so I see each panel itself being modified to create a color scheme.
Other than that, anodization is a possibility. The Romulan ships (TNG) always looked anodized to me.
Every time I hear this I CRINGE.
"Transparent aluminum" is a scientific impossibility. Sort of like "Cold superheated gas."
The very characteristic which makes aluminum METALLIC (loosely bonded free electrons) is also what makes it (and all metals) OPAQUE.
There is NO SUCH THING AS MOLECULAR STRUCTURE WHEN TALKING ABOUT A METAL!!! Metals, BY DEFINITION, do not have a "molecular structure" and thus you cannot adjust the molecular structure of a metal at ANY level.
Yes, you can make CERAMICS based upon aluminum which would be transparent... but they would not have the tough, malleable characteristics of metals, and thus would be useless for that purpose.
For a substance to have metallic properties, it must have "free electrons." Free electrons reflect photons very effectively... that's why metals tend to be shiny. The more free electrons, the more shiny it is (Mercury has a LOT of free electrons, which is why it's fluid at room temperature and EXTREMELY shiny).
This particular line in ST-IV annoyed me at the time... and since so many people have accepted it without question (by the way, it was a POLYMER CHAIN which was shown on-screen... unrelated to either metals or ceramics!), there's a lot of really bad science accepted as "fact" by Trekkies.
If there was only one thing I could "retcon" out of Trek's existence, I really think that "Transparent aluminum" would be at the top of my list!
(RANT MODE: OFF)