FWIW you get the same on Linux by installing stuff in /usr/whatever/wherever, /usr/local/whatever/wherever or /opt (which is the closest to Program Files-like p

FWIW you get the same on Linux by installing stuff in /usr/whatever/wherever, /usr/local/whatever/wherever or /opt (which is the closest to Program Files-like place) and making symlinks to the "global" binaries (those meant to be accessible via the shell) while keeping everything else in the application-specific folder. It isn't very uncommon to see binaries inside /usr/bin being symlinks to binaries in other directories, even if you stick with distribution-only packages.