I can't believe it took me almost 2 years to stumble upon this fix. I noticed that the first run of IWAR has no scaling problems, and on a hunch I believed they were caused by the glide wrapper. The glide wrapper settings get initialized on the first run of the game, so the second time you run it'll use the settings that cause the scaling problem.

When I delete the glide_wrapper.zbag file in my ~/AppData/Roaming/ folder the scaling problem goes away for the next time I open the game.

I simply created an empty text file with the name "glide_wrapper.zbag" and set it read only. Now the game runs with the correct scaling all the time.

TL;DR: Delete the contents of your glide_wrapper.zbag and set the file read only.