The last thread pretty much summed it all up well except one point which is probably relevant to your initial post. Noise. I would never use poly anywhere it didn't get siliconed, or caulked ever again.
In the past I always used acrylic for the cub windows. Last time I used Lexan, and for the D windows that was probably fine. In the door it is not 'glued' in so to speak, and it rattles against the frame, and the noise it makes is very tinny and horrid. I keep meaning to put felt or cork washers between the window and frame where the screws go through to see if it helps, but as is it makes more noise than the typical metal belly cub... boo
For silicone / caulking, the clearest I have found is either Lexel, or Sika flex.
Take care, Rob