Is there some reason you cannot just set the output scale? This almost certainly already does what you want. If you're talking about X11 applications running on XWayland, I think you can still change the properties there with xrandr.
No, I'm not using XWayland.
I edited my comment above after you posted -- the Wayland protocol unfortunately does expose the screen size in millimeters to the client. I'm pretty sure Chromium and QT use this, which is why I need to lie to them.
Another question: is there any sort of "Wayland socket proxy"? Like a stupid simple program that offers up a $WAYLAND_DISPLAY socket to a client, opens its own to a server, and then passes all results through unmodified? It would be really easy to hack a change like this into a proxy like that, but I can't seem to find one. Sort of surprising; the simplicity of the Wayland protocol makes it seem like such a thing should exist. Sort of like waypipe, but without the cross-network magic.
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...