I think you can merge multiple directories onto /usr/local using overlayfs.

That seems to be what Stow is simulating, using symlinks.

Symlinks have the advantage that they persist; you don't have to recreate them after every reboot.

Stow also has ignore lists, which isn't something overlayfs will do, or not nicely; it is oriented toward directories. In the package installation use case, you could just keep unwanted cruft out of the individual installation directories that are being combined.