You could use reshade's border shader to black out a couple rows of pixels at the top of the screen. Setting the size ratio to 2.41 seems to do the trick at 3440x1440
Oh, very strange. I do have the steam version as well. Since I purchased on humble, I'll download the DRM free version as well to test and report back.
EDIT: It's still not working with the Humble version. I also tried running true fullscreen at 2560x1080 with the correct width for said resolution and it still isn't working. Is there anything I can do to help you figure this out?
It's broken for me as well, though the "internal_size_w" parameter isn't the problem. That said, the correct value for 3440x1440 is 1720, not 1707 (2560x1080 and 3440x1440 are both referred to as 21:9, but they aren't actually the same aspect ratio, nor are either of them actually 21:9, hilariously). With 1707 in the file, you will see a small and pretty insignificant sliver of black bars at the left and right side of the screen.
This lighting issue is likely a problem for everyone.