Interesting, but there must be some difference. The default options were automatically chosen for my compile and the compiled version ended up with a broken phonon backend audio system. For future reference I had to move phonon_vlc.so out of /usr/local/lib/kde4/plugins/phonon_backend/ and compile phonon-xine to keep systemsettings>multimedia and knotify from crashing. It also prevented all KDE system sounds until I did this.
For comparison, the packaged version had none of these problems.
edit: There are also differences in the KDE power settings. The packaged version does not work well this time. It says the power management configuration module could not be loaded. The compiled version works fine.