This is very true, more so of the Debian based distro's.
Exim is a worst case example I think in Debian. The Debian stuff is STILL at V3 which hasn't had any developer support for over four years. The devs even setup a separate maillist just to cover then and stop the main list getting drowned in V3 questions which people can hardly remember anymore.
It also doesn't help that alot of packages make up their own directory layout and can be difficult to place in other ways. and again the distro's have their own layout which they config the package into - eg package1 uses /usr/local/package1 by default; package2 uses /usr/local; distro one puts things in /usr, distro 2 puts things in /usr/sfw....
it's a mess and this needs sorting out not just for linux based systems for for the Unix world in general.