Thanks for the review!
Well, unfortunately in this instance, it was the only trans-red element I could use. I really didn't want to have to put solid red brick in there or try to SNOT the 1x2 plates on somehow and lose the transparent effect. I wanted to preserve as much of the trans-red look as possible, so this is what I decided to go with. I would much rather have had some 1x2 brick or even some trans red thin walls.
Just as an FYI, these trans neon green 2x2 rounds are not necessary to the design of the fighter. LEGO added them so the model would pass the heat test. Personally, I suggest removing them since the model stands up just fine on the landing gear. Just don't put it in the oven. ;-)