IMHO the best way to do this is to install apps in the Applications subfolder of your user directory. When you do this, Launchpad and everything else treats them as if they were installed in the /Applications folder, but it's still trivially easy to tell what you need to migrate to a new machine.
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.
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".