Okay so year, opened up the textures on a couple of FPSCR partial transparent objects, and they are done here the same as a lot of other game engines. Where you must change the Alpha Channel, making it half way between black and white colour will modify how transparent a surface is.
Here is the Alpha channel from the Plastic Red Crate which is default box type in FPSCR. Notice the white is 0% transparency, and the black is 100% transparency. If you modify it so you have the grey colour exactly half way between fully black and fully white, you'll get 50% transparency, then depending on RGB channel, it will appear a certain semi transparent colour.
I believe however, once the engine is further a long there will be materials you can enter, such as glass, but not sure how they work exactly, never gone more advanced then this before.
Update: Been trying this out, I can't get partial transparency, only complete. Not sure if I am exporting my .dds wrongly or if the engine just doesn't support it.