I am having this exact same issue as well, but it isn’t limited to HDMI; I am seeing it on DisplayPort (DP) too.
My desktop UI looks fine, but Proton is broken, games cannot see the real physical resolution of my monitor.
Native Resolution: 3440 x 1440
Scaling: 150%
Result: xrandr shows the resolution as 5160 x 2160 (which is 3440×1.5).
This worked perfectly on my previous Hyprland (Omarchy) setup with the same scaling, but on COSMIC, the logical scaled resolution is overriding the physical one for Proton/XWayland applications, making the native resolution unavailable in-game.