[neurobashing]

on Sequoia, it's already separated. Apps shipped as part of the OS live in /System/Applications, and stuff you install (however you do it) are in /Applications.

[radicality]

What’s meant to go under /Users/<username>/Applications ? If I’m the only user of the machine is there a difference between that and /Applications ?

Looks like for me the only thing is Jetbrains IDEs installed themselves there hmm.

[neurobashing]

I think for the average user it's more of a remnant of NeXTStep. It is galling that Little Snitch doesn't let you use a supported feature; but I think Apple doesn't really care about ~/Applications any more, since they "solved" it w/ the Applications and System/Applications "split".