The first point here is weirder than just "the game defaults to fullscreen" because it doesn't. It defaults to borderless, which is good. The issue is that the borderless setting doesn't remain consistently borderless. While borderless fullscreen is selected, the game's loading screens - including the one which appears on launch - cause it to enter dedicated fullscreen instead of borderless. When it does this, it also resets the system resolution to its default setting (in my case, 1080p). If that resolution is smaller than your system's normal resolution, this reset is applied to the background, and deforms any window which is too large to fit in the new resolution, shrinking and distorting them in weird ways. This is particularly problematic on apps with fixed-ratio windows, which it can deform in ways which break the app, and maximised windows, which often get repositioned awkwardly while trying to reset them into a proper maximised state.
EDIT: Turns out the problem is worse than I realised. No matter what, the game sometimes randomly sets itself to dedicated fullscreen when you finish a run, or when you're on a loading screen for something else, then resets itself into borderless. And yes, this has all the problems mentioned above with the fullscreen mode forcing your system resolution to change and breaking any windows open in the background.