kde 3.5.7 is now available in debian unstable on several architectures. Hopefully the rest will catch up when some bugs in other packages are fixed. Feel free to upgrade – but please please please – log out of kde and…

It seems that the main source of the configuration variables is in the CMake-files. Especially kdelibs/cmake/modules/FindKDE4Internal.cmake. Instead of the automake –sysconfdir, it seems you can use -DSYSCONF_INSTALL_DIR=/etc at least in kde. This does not seem to be CMake specific, but…