I've done some transparency in steering wheels and such, but Orion taught me that for windows, you're better off just leaving open air where the windows should be. What I've done for transparency though is to paint it in the editor with a color you definitely won't use anywhere else in the plane (I tend to use hot pink or bright purple). Then, I'll go into Gimp and find the exact RGB of that color, and then use the color-to-alpha tool and turn everything that color transparent. Once that's done, go over with some grays and light blues and draw lines consisting of individual pixel dots, so it resembles vanilla Minecraft glass. I did that for windshields on a few cars and I think it looks pretty good (but I'm way too lazy to do it for every plane and car lol).
The windshield there is transparent. The most annoying part though is that BOTH sides have to be done the same (I like to draw in the gray/ blue dots on one side and leave the other blank). Also, it looks kinda weird when you look really closely at the edges inside the glass areas, but most people probably won't notice that.
Hope that helps! I'm LOVING your progress! I wish I had the patience and talent to make something that detailed!