Qt applications are almost certainly using the output scale property, I've tried those recently. I haven't tested Chromium's wayland backend recently, but Chromium is ignoring those physical values: https://github.com/chromium/chromium/blob/99314be8152e688baf...
Maybe your chromium is not using the Wayland backend correctly? If a Wayland application is using the physical values to determine scaling, instead of the output scale, that's a bug and you probably should consider reporting it. It's probably a mistake that the physical size information is there, it's unreliable as you have seen.
Edit: Rather than messing around with proxies, if you want to do a quick test to confirm, you could simply hack wlroots here to send a constant value: https://github.com/swaywm/wlroots/blob/b3e76d667855c16e97a4d...