I can confirm that --bindir and --libdir are broken in Python 2.6.2,
despite the fact that ./configure --help lists them as helpful options.
 At the very least, ./configure should complain if you're using options
that don't do anything!  That would be the easy fix.

Here is what I am doing:

./configure \
    --prefix=/home/soundmurderer \
    --bindir=/home/soundmurderer/bin/x86_64/Python-2.6.2 \
    --libdir=/home/soundmurderer/lib/x86_64 

OK, now let's see the relevant section of the generated Makefile:

# Install prefix for architecture-independent files
prefix=         /home/soundmurderer/auzilov

# Install prefix for architecture-dependent files
exec_prefix=    ${prefix}

# Install prefix for data files
datarootdir=    ${prefix}/share

# Expanded directories
BINDIR=         $(exec_prefix)/bin
LIBDIR=         $(exec_prefix)/lib
MANDIR=         ${datarootdir}/man
INCLUDEDIR=     ${prefix}/include
CONFINCLUDEDIR= $(exec_prefix)/include
SCRIPTDIR=      $(prefix)/lib

# Detailed destination directories
BINLIBDEST=     $(LIBDIR)/python$(VERSION)
LIBDEST=        $(SCRIPTDIR)/python$(VERSION)
INCLUDEPY=      $(INCLUDEDIR)/python$(VERSION)
CONFINCLUDEPY=  $(CONFINCLUDEDIR)/python$(VERSION)
LIBP=           $(LIBDIR)/python$(VERSION)

So, the --libdir and --bindir flags had no effect on LIBDIR and BINDIR,
and I wind up editing the Makefile by hand to get desired behavior.