On Sway entering fullscreen using the 'F' keybind makes the window fullscreen, but renders at the old windowed size. Starting in fullscreen using the :fs parameter works correctly, as well as making the window fullscreen through the window manager.
This is probably a bug in SDL, because it keeps reporting the old window size both in the SDL_EVENT_WINDOW_RESIZED event and also when calling SDL_GetWindowSizeInPixels(). This only happens when running through XWayland, which SDL3 does by default.
As a workaround SDL can be forced to use the wayland backend where fullscreen behaves correctly using the environment variable SDL_VIDEO_DRIVER=wayland