I tried running this command rpm -U --prefix /data1/builds/1 \ htdocs-redirect-emc-2.48-2.src.rpm I have a topdir setup in /data1/builds/1 and the files did not go into /data1/builds/1/SOURCES and /data1/builds1/SPECS I use RPM version 2.5.6 so this may be fixed in your sources already.
The --prefix option supplies a new leading path for a tag in a binary rpm containing that contains the old leading path and absolute path names. Since src.rpm's contain relative not absolute paths and do not contain a prefix tag at all it's unclear whether the effort involved in implementing --prefix is worth the effort. Meanwhile, try rpm --define '_topdir /data1/builds/1' -U ... which should have the desired effect.