I'm also using a tiling wm (i3), but I never had this problem with this game, which wine/proton version do you use? Some custom wine builds sometimes have "fullscreen hacks" of sorts, which may be the reason it's behaving odd in windowed mode. I remember Lutris having some of those wine builds. Consider trying different Wine or even trying Bottles as a prefix manager instead of Lutris, I find it more convenient and more up-to-date on available wine/proton releases. You will have to install it from Flatpak, however, which is a downside.