Edit: There are also many easy to use front ends for adding mods and working with different minecraft versions etc.
* Because your patches only work against one version of the game.
* Because you are directly updating files, so both of the previous restrictions can easily be violated, which tends to cause a crash on startup.
The front-ends work around this lunacy by keeping multiple clean copies of the entire install, at multiple version levels, so that each mod can trash it on its own or use the version it needs.
There's no way I could have single handedly managed the 500+ game server instances with out something like that.
As an aside, if you've never had to deal with any of the CoD series servers count yourself very lucky. I think it was still a requirement for CoD3 that the windows dedicated server required directx installed..... just so it could show the splash screen.