Maybe the problem is saying all programs have to behave the same. It would indeed be irritating to have every unix-tool link to it's own libraries. But most well-known tools are small programs that don't get constant feature updates. But it's a whole different thing for typical desktop applications. Those are often way more often updated than the distros and there's no 2 distros out there having the same library versions which might be needed for an app to run. Still distros do not like if such applications use separate library versions... and that just doesn't work so well except maybe for the handful of high-profile applications which have enough maintainers. I mean even keeping an up-to-date Iceweasel on Debian already caused me trouble with library dependencies just some months ago - and that is probably the most prominent desktop application in the free software world.
It's getting even stranger in the world of free games. When games need library fixes (very typical situation as games and engines are very interwoven), which are not yet in a distro (and won't be for some time because the library is for example not yet officially updated or maybe a certain patch simply won't be included). On a system like Windows it's no problem - modify the library source and add the dll. On Linux distro's... well, just not easy possible. Which means funny enough that it's easier to modify library sources in the in the proprietary microsoft world than in the free software world. We got freedom coming with library + distro gatekeepers so to say... which pretty much sucks (even for the library authors).