This was discovered by looking at Debian's package, where they create an installation like this:
$(MAKE) DESTDIR=$(CURDIR)/debian/tmp INSTALL_GROUP=root LIBPATH=/usr/lib/$(DEB_HOST_MULTIARCH) PREFIX=/usr install -f makefile.share
In my case, DEB_HOST_MULTIARCH = x86_64-linux-gnu, which makes complete sense with regards to Debian policies. However, because libtomcrypt.pc.in has a hard coded libdir=${exec_prefix}/lib, the resulting system pkg-config (/usr/lib/x86_64-linux-gnu/pkgconfig/libtommath.pc) isn't useful.