Till: well, have you tried setting your system locale to something where A4 is actually used?
The primary method for setting paper sizes is always going to be the locale. glibc provides support for LC_PAPER; CUPS keys off the locale string -- there really is no need for an extra (conflicting) mechanism to find out which paper size to use.
I understand that CUPS has support for libpaper (IMHO needlessly). Adding support for this to system-config-printer would mean creating Python bindings for it as there do not appear to be any currently. It is not something I am prepared to spend any time on. I just don't see the benefit.