I want to install a set of software organized into directories at the root level.
Is there any method in which I can use pacman to install certain packages into a directory of my choosing?
Yes, that's possible, by specifying a different root location,
-r, --root Specify an alternative installation root (default is /). This should not be used as a way to install software into /usr/local instead of /usr. This option is used if you want to install a package on a temporary mounted partition that is "owned" by another system. NOTE: if database path or logfile are not specified on either the command line or in pacman.conf(5), their default location will be inside this root path.