If we can require applications to draw their own window controls, I think we can ask them to handle their pixel densities.

that's a good point. window controls should be at the proper scale too.

It's not transparent on Wayland or Windows (no idea about mac) either if you want actually properly drawn stuff.

Well, ok, on Windows if you keep to certain standard elements of Windows API and only use standard widgets you could get close to transparency.

It'll not be transparent to an application using basic X APIs, but nothing prevents a higher level UI toolkit from implementing it properly.