Interesting I don't use spaces much other than an occational fullscreen video. I really have given them a lot of attention over the years and experimented with all the differint changes since they interoduced it and with Command+Option+H and window mover shortcuts they never really seemed to help make things faster or cleaner for me so I wonder if there is an issue there. There use to be an option to show Finder in All Spaces but that has since gone the way of the Dodo Bird.
Glad you got at least mostly what you wanted. Always good to know when to throw in the towel and not an easy thing to do. I downloaded HazeOver since it is included with Setapp subscription.
Though another third party app I currently use Magnet for this. There are many windows management apps out there and I have likely tried them all. About 15 years ago there was nothing after 100+ hours of searhing and so I wrote my own.
You might be interested in these macros which can save a window position.
Though not directly what you are asking it might give you some ideas for restoring things.