I don't know why I didn't think of this before, but I made cut outs for the windows, which would make the canopy appear thinner on the outside, and yet not compromise rigidity too much. Also, it would allow someone to glue clear plastic inside and hide the marks.
Might want to play around with Tinkercad. It's amazing what you can do just adding and subtracting primitive shapes. It's also designed to import and export Stl's natively. It's free as well, which is a bonus. I use Lightwave myself, and Fusion 360. Lightwave is pricey, but you can get a hobbyist version of Fusion 360 for free for 3 years.