I feel silly for not thinking this… It works fine without the mod unless you try to change resolution/fullscreen settings.
Apparently the mod is supposed to disable in-game resolution controls and force it to borderless window at monitor resolution when the flipmodel swapchain is enabled (which is necessary for hdr). It seems to do this by always launching the game in a 720p window and depending on if the custom swapchain is enabled it either resizes it to the screen or applies the in-game resolution setting. Gamescope doesn’t respond to the change and keeps outputting 720p in a 1440p window :/.
I can’t wait for wine wayland
Edit: Just found that using the --force-windows-fullscreen option fixes this issue!!