The LED buttons like your Spectralite series use a different plastic for the plunger body and diffusers than for the bodies of the buttons.
Not entirely. The caps on the plungers are the very same material as that of the body. It's likely that those caps are part of the same multi-cavity molds, for the same reasons of color matching, etc... But there may be a chance that production is high enough for those caps have their own molds, and run on a different machine. One reason that injection molding companies don't like to do this for smaller runs (<20,000 units at a time) is that it is inefficient unless dedicated to a press. Having to change out these molds and re-set up machines takes time and effort to tune them in, and having one mold with all of the pieces of the same color related that particular item, means
one setup, larger batches in material dryers and lower production costs.
Also to keep in mind is that parts don't always come out of the molds perfectly, and over time, a company can build up a surplus of less problematic parts. The caps, being smaller parts, probably mold more reliably than the bodies, and extras can be used with a different button design (like the black one you pictured). But again, the quantity of molds / presses being used really depends on the scale of production.
With at least 3 different types of plastic per button (4 if you count the black LED/switch holder), would they still use only one mold? 
No. The same switch holder is used on just about every lighted button from that manufacturer. So it would make sense to mass produce these on their own. The diffuser element is also likely used on other lighted buttons with the same size plunger.
As for small runs of special colors, that wouldn't be the first time IL has done this. They, and other manufacturers, will sometimes entertain small orders, possibly at costs lower than their production costs, to have others explore the possibilities of new markets. Their transparent colors line seems to have started out this way long ago as a request from one individual (from here, no less) and when it looked like there was a market for them, they sold them to anyone through HAPP, pretty much negating the prospects of future sales for that individual. Something similar happened when they knocked off the properties of our ElectricICE buttons, after we established the market. I actually approached IL with the ElectricICE concept before resigning myself to having our own (expensive) molds made, and they flatly refused to have anything to do with the idea. Of course, this was before they lost HAPP's business, so things could be different today. Now they supply their own translucent white version to at least two other vendors, likely after being approached by one of them initially. In retrospect, it was just as well things went this way, as it afforded opportunities for us to design a button with more diverse options, and opened the doors to produce other colors at our whim. But I digress.

Anyway, if those special colored buttons prove not to be big sellers, they would most likely not run them again. But that's obviously for them to decide.