Some of the reasons to use packages are consistency with policies. For
example, most distributions disallow packages from owning any files below
/home, and require that operation of the software not require /usr to be
writable at all times, and various other requirements. As such, logs
cannot actually reside under the same parent directory as binaries. The
packages provide symlinks to the real locations, so things look the same
taking into account the difference in BBHOME.
If the packages don't get maintained going forward, I'd end up having
to migrate to source-based, and that would involve hand-tweaking the
rpm-based locations.
Well, once I have more than one installation of software, I package it
myself anyway, as maintaining a package becomes less work at about the
3rd installation. If I no longer maintain packages (although I do), that
*really* doesn't mean that you would need to switch, you should consider
rebuilding the SRPM ...