Here's my proposed patch, along the lines you suggested. top_srcdir didn't seem to be set, so I used srcdir instead.

Bootstrapped on x86_64-unknown-linux-gnu



2011-06-04  Douglas B Rupp  <r...@gnat.com>

        * fixincludes/configure.ac (host_makefile_frag): Use mh-interix.
        * fixincludes/configure: Regenerate
        * fixincludes/Makefile.in (FIXINC_CPPFLAGS): New flag macro.
        (@host_makefile_frag@): New substitution placeholder.
        (.c.o): Use FIXINC_CPPFLAGS.

diff -rupN gcc.orig/fixincludes/configure.ac gcc/fixincludes/configure.ac
--- gcc.orig/fixincludes/configure.ac   2011-04-06 17:01:09.000000000 -0700
+++ gcc/fixincludes/configure.ac        2011-06-04 13:18:23.000000000 -0700
@@ -23,6 +23,20 @@ ACX_PROG_CC_WARNINGS_ARE_ERRORS([manual]
 # Determine the noncanonical target name, for directory use.
 ACX_NONCANONICAL_TARGET
 
+host_makefile_frag=/dev/null
+if test -d ${srcdir}/../config ; then
+case "${host}" in
+  *-interix[[3-9]]*)
+    host_makefile_frag="config/mh-interix"
+    ;;
+esac
+fi
+
+if test $host_makefile_frag != /dev/null; then
+  eval host_makefile_frag=${srcdir}/../$host_makefile_frag
+fi
+AC_SUBST_FILE(host_makefile_frag)
+
 # Specify the local prefix
 local_prefix=
 AC_ARG_WITH(local-prefix,
diff -rupN gcc.orig/fixincludes/Makefile.in gcc/fixincludes/Makefile.in
--- gcc.orig/fixincludes/Makefile.in    2011-04-06 17:01:09.000000000 -0700
+++ gcc/fixincludes/Makefile.in 2011-06-04 00:31:30.000000000 -0700
@@ -32,6 +32,11 @@ WARN_CFLAGS = @WARN_CFLAGS@ @WARN_PEDANT
 LDFLAGS = @LDFLAGS@
 INCLUDES = -I. -I$(srcdir) -I../include -I$(srcdir)/../include
 FIXINC_CFLAGS = -DHAVE_CONFIG_H $(INCLUDES)
+FIXINC_CPPFLAGS =
+
+#### host specific makefile fragments come in here.
+@host_makefile_frag@
+###
 
 # Directory where sources are, from where we are.
 srcdir = @srcdir@
@@ -73,7 +78,7 @@ default : all
 # Now figure out from those variables how to compile and link.
 
 .c.o:
-       $(CC) -c $(CFLAGS) $(WARN_CFLAGS) $(CPPFLAGS) $(FIXINC_CFLAGS) $<
+       $(CC) -c $(CFLAGS) $(WARN_CFLAGS) $(CPPFLAGS) $(FIXINC_CPPFLAGS) 
$(FIXINC_CFLAGS) $<
 
 # The only suffixes we want for implicit rules are .c and .o.
 .SUFFIXES:

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