Thanks to /u/[email protected] for mentioning KDE window rules. In KDE, we can add rules for windows so that they behave in specific ways. One rule that can be added is the position: remember rule, and it’s possible to make that rule apply to all windows by removing the match field. This way, closing and reopening windows keeps them where they were.
This is a very typical complaint about wayland that a lot of people have, something that apparently worked natively with X11 and annoyed me to no end since I had to position all the windows every day when logging into my desktop. No more! I hope this helps :)
There is definitely this for activities, so I’d be surprised if there isn’t for virtual desktops given how much more popular/supported they are