pkg-config files are arch-dependent (due to libdir usage), so use arch-dependent location.
--- xen-4.9.0/config/Paths.mk.in.orig	2017-06-27 20:13:19.000000000 +0200
+++ xen-4.9.0/config/Paths.mk.in	2017-07-31 20:59:29.558580546 +0200
@@ -57,4 +57,4 @@
 XEN_CONFIG_DIR           := @XEN_CONFIG_DIR@
 XEN_SCRIPT_DIR           := @XEN_SCRIPT_DIR@
 
-PKG_INSTALLDIR           := ${SHAREDIR}/pkgconfig
+PKG_INSTALLDIR           := ${libdir}/pkgconfig