I've just learned of the following threads:
Proposed iLiad Packaging/Installation Standard
iLiad 3rd Party Program Standardization
Looks like this structure was actually not "God-given" but merely the result of a lenghty discussion some months/years ago. So the first-gen developers voted for the symlink version.
But as the iLiad OS project evolves, maybe we can re-partition the root file system in some time to give / some more space to hold user apps. But that has to be seen.