on my computer i select the windows i want to share. each of those windows could be sent in a separate stream to the remote machines. and likewise my computer could receive independent streams of multiple windows. this way i could arrange all windows as i see fit.
the alternative is that the app takes over a full screen and the shared windows are rendered within it. then the app is responsible for window placement and can implement its own way to arrange windows as it sees fit, and share that location with its peers. a window manager within a window manager, of sorts. something that many windows applications like photoshop already do. linux/unix could do that with Xnest already more than 30 years ago. nowadays there is also xpra, which can mirror windows across multiple screens. i don't know about wayland, but i believe it should be possible there too.