The first hunk fixes the install location of the pkconfig files:
  FreeBSD installs pkgconfig files to $LOCALBASE/libdata/pkgconfig
  qmake uses QMAKE_PKGCONFIG_DESTDIR as relative path to $$QT_LIBDIR.
  As this is now '${PREFIX}/lib/qt5' we need to go up two levels.

The second hunk stops qmake from generating la files.

--- mkspecs/features/qt_module.prf.orig	2016-09-16 05:49:42 UTC
+++ mkspecs/features/qt_module.prf
@@ -247,7 +247,7 @@ load(qt_targets)
 # this builds on top of qt_common
 !internal_module:!lib_bundle:if(unix|mingw) {
     CONFIG += create_pc
-    QMAKE_PKGCONFIG_DESTDIR = pkgconfig
+    QMAKE_PKGCONFIG_DESTDIR = ../../libdata/pkgconfig
     host_build: \
         QMAKE_PKGCONFIG_LIBDIR = $$[QT_HOST_LIBS]
     else: \
@@ -267,7 +267,6 @@ load(qt_targets)
     QMAKE_PKGCONFIG_INSTALL_REPLACE += pclib_replace
 }
 !lib_bundle:unix {
-    CONFIG += create_libtool
     host_build: \
         QMAKE_LIBTOOL_LIBDIR = $$[QT_HOST_LIBS]
     else: \