I've grepped through the entire tree and can't see how the configure variable with_multisrctop is ever set to anything than itself.
It looks like an anchronism left over an earlier day before multilibbing became more common. Worse there are all sorts of hoops that every directory's configure script needs to jump through in order accomodate this variable that appears to never be set. My guess is that at one point there were target specific directories in the toplevel of the source tree, but those are no longer present. Anyone have any enlightenment, anyone still using it? For example of hoops, see libiberty configure script which attempts to determine where install-sh is located via series of if/then/elses and sets that to ibiberty_topdir. Note that this doesn't actually really work that well as intended since it passes this value to AC_CONFIG_AUX_DIR($libiberty_topdir), isn't designed to accept shell variables, so a directory with the actual name "$libiberty_topdir" is created in the libiberty directory if you run autoconf.