Earlier quoted context omitted.
One thing that has stood out to me is that when I have two Edge windows open, for example and I switch to the last used window from Safari, both windows overlap instead of just the one window I was working with.
If you want to just have the one window come forward use Expose to do it, rather than Cmd-Tab or the Dock.
Apple for some reason avoids giving people too many options. Just one option: "threat windows of the same application independently" with a default of no would make everyone happy.