I agree that more distinct windows will help when there are many of them on the same workspace.
Currently now default terminal emulator in #gnome and #builder support choosing one of a few predefined colour pallets, maybe this should be standardised so per app level we can always select theme and on desktop light/dark mode?
But for that to work in #flatpak probably #xdg_desktop_portal would have to be proposed, so... it would be quite some time before we could even see it.
Unless those pallets would be baked in into #adwaita but that would be suboptimal, and probably not desired to not introduce breaking changes if supposed portal finally came to existance and would require changes to current behaviour.