You're just re-describing the behaviour I already described as irritating; did you perchance reply to the wrong comment?
Scenario: I'm in a terminal doing something, and I have a second window I'm switching back and forth between that contains the man page for a command. In isolation, I haven't given you enough information to tell whether I should be pressing opt-tab or cmd-tilde to swap windows: maybe the man page is in a browser, or maybe it's in a second terminal.
Scenario: I'm switching back and forth between an editor and some reference document in another window; you can't tell which key I should press to swap without knowing if I'm looking at the document in another editor instance or a browser window.
Scenario: I'm switching back and forth between a terminal and some reference document from a cloud provider. You can't determine which key to press to swap without knowing if I'm ssh'd in a terminal or using a web-based cloud terminal.
Scenario: I'm switching back and forth between an image editor and a client's low-resolution logo they emailed me. You can't determine which key to press to swap without knowing if I'm looking at the reference image in another image editor window or a browser.
There are some apps that change that behavior if you want. [0]
I didn’t reply to the wrong comment, I was just trying to be helpful.
This OS behavior has seemed second nature to me ever since browsers implemented tabs. Like in each of your described scenarios I usually forget which browser tab is in the foreground when I switch, I will have to Ctrl+tab until I find the relevant one. It will stay on top once I do though.
That is what MacOS does; the window of an app you had in focus last will stay on top of the stack. It makes intuitive sense to me personally but I agree it does make finding stuff a little onerous.
In your scenarios, you know which applications you have your relevant documents opened in so once you have them on top switching is easy. But again, I understand that a decade of muscle memory and using a different paradigm will make this behavior infuriating.
^ b/c of this, I actually like how MacOS separated app and window switching. It's a bit more fine grained, and I can use either of the two depending on the specific intention.
that doesn't actually solve the OP's problem as it still requires you to be aware of all your windows and which ones are in current app vs which ones are in different apps.
I bound it to Option + tab though, more intuitive to me.