Although that may be intuitively obvious to you, could you put that in laymen's terms for the rest of us?

A texture is a picture + an Alpha channel which defines what part of the picture is transparent and which is not. The Alpha is usually the same as the picture, but in black and white only. Normally, black means transparent and white means opaque, it was like that in FS9 and in FSX SP1.
Now in FSX SP2 this is the contrary. White means transparent and black means opaque.
So you simply have to use a tool nammed DXTBMP, edit the texture of the canopy glass and make so that it's Alpha channel gets inverted, like a negative. It takes approximatively 10 seconds once you're used to the procedure:
- open the texture
- export Alpha to editor
- make Alpha Darker in editor
- save in editor
- refresh Alpha in DXTBMP
- save in DXTBMP, choosing "extended bitmap", then "DXT3".
The problem is that between (FS9 and FSX SP1) and (FSX SP2), the "transparency" has been inverted.