What you are saying is not correct; the xdg-desktop-portal API is not tied to flatpak, it has support for individual windows, it's generic and can be re-used by any sandbox, and it can also be used outside a sandbox. (Snap I believe is using it and it should be not too hard to get it working in other tools like firejail either) Using it has the benefit that your application will also work inside a sandbox and doesn't need to have additional code paths for X11 and wayland and for the sandboxed case. See here for the description of libei, it's not ready yet but is being worked on, and should have a similar design that allows it to work correctly in a sandbox: https://who-t.blogspot.com/2020/08/libei-library-to-support-...

In almost all cases, Wine should viewporter or use fullscreen-shell to set custom resolutions for specific programs, the only reason you would need to allow wine to have access to an xrandr-like API is if you wanted to run your monitor configuration tool from windows, which I strongly doubt people are wanting to do that. If you are using GNOME/KDE, the GNOME/KDE control panel is always going to be the most reliable way to configure that.

Yes you would need to track upstream and keep up with their unstable APIs in order to write such a library that but that's no different than if you asked upstream to do it, they would just be doing that in their tree. (In some cases this is what they do anyway with the xdg-desktop-portal) In any case you would need to be more specific about what it is you want because just saying "implement everything from X11 exactly the way X11 does it" is not useful, that's never going to happen, so let's focus on what actually it is that is needed.