[rekado]

A disadvantage is that some services (like dbus) look for service files in a well-known location. When packages are installed they don't place any of their files in a directory outside of their target directory. So, JACK2, for example, won't be able to place its dbus service file in a location that the dbus service natively knows about.

In many cases situations like this can be fixed by setting environment variables, but in some cases more patching is required to make this work properly.

EDIT: I don't consider this a serious disadvantage, though. It is not unusual for packagers to patch software in other distributions. (I dare you to check out spec files for popular RPMs.) It's just something a package maintainer has to think about under some circumstances.

I should also note that I'm surprised at how little patching is required for most software (besides the common shebang patching).