Glad to see someone is looking at it :-)
Fullscreen mode in SDL2 does seem a bit flaky - window borders change or disappear when switching back for example. And the documentation isn't very clear on how it selects the screen resolution. In my case it preserves the aspect ratio (I get black bars on the left/right), but that could just be on my monitor size/resolution.
SDL2 does have a "fake" fullscreen mode where it leaves the desktop resolution as is, and expands the window to cover the screen. From some basic experimentation this seems to work quite well. It fixes the window border issues and should leave the aspect ratio unchanged, as it doesn't actually change the screen resolution.
So I'll probably put out a patch to use this mode instead soon.