If I've one frustration with computer interfaces, dating back to the 1990s, it's this. If anything it's become worse with time as apps, both desktop and mobile though especially the latter, become more self-centric, to the point of having their own, non-filesystem-based, data silos. I understand some of the security reasons for this (apps are themselves increasingly untrusted and untrustworthy, and data-sharing is a significant risk). But it is extraordinarily frustrating when trying to work with multiple tools.
Modern MacOS is particularly pernicious in that I'm often working between multiple applications, but on the same project, and the friction of raising and lowering all app-associated windows as I cycle between these, often navigating to a workspace I'd not meant to go to, is quietly maddening.
The Linux / X-Windows notion of focus-follows-mouse addresses this somewhat. Your current app is whatever the mouse happens to be on top of. On MacOS this simply isn't available, though there are some ... hints of this. E.g., if I happen to have the mouse over a browser window I can scroll that window with the mouse. But if I then, say, hit Cmd-W to close that tab ... suddenly the actually focused app which I'd forgetten about gets a kick in its nethers. This happens to me several times a week, if not per day.
I don't know that Stapler is the true solution to this, but it does seem to track in that direction.