I have just very recently had problems with graphite optimizations. Because Perl modules appear to ignore the CFLAGS in /etc/make.conf I could not have got around the problems without help, see http://forums.gentoo.org/viewtopic.php?p=6260599#6260599.
I expect flags in /etc/make.conf to be honored except when explicitly overridden.
First, if a package can't handle the graphite optimizations (or any other use of CFLAGS), perhaps the build for the package could just quietly turn off the particular compiler flags that it can't handle.
Second, if the first is not done, at least honor the flags in /etc/make.conf. At least some perl modules violate this rule, instead using the flags last used in compiling perl.
Finally, xorg-server fails to emerge when using the graphite optimizations with many errors like:
../doltcompile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../include -DHAVE_DIX_CONFIG_H -Wall -Wpointer-arith -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -fno-strict-aliasing -Wbad-function-cast -Wformat=2 -Wold-style-definition -Wdeclaration-after-statement -D_BSD_SOURCE -DHAS_FCHOWN -DHAS_STICKY_DIR_BIT -I/usr/include/freetype2 -I/usr/include/pixman-1 -I../include -I../include -I../Xext -I../composite -I../damageext -I../xfixes -I../Xi -I../mi -I../miext/shadow -I../miext/damage -I../render -I../randr -I../fb -fvisibility=hidden -O2 -march=native -ftree-vectorize -floop-interchange -floop-strip-mine -floop-block -pipe -MT cursor.lo -MD -MP -MF .deps/cursor.Tpo -c -o cursor.lo cursor.c
cursor.c: In function 'RealizeCursorAllScreens':
cursor.c:170: sorry, unimplemented: Graphite loop optimizations can only be used if the libcloog-ppl0 package is installed
In my case (amd64) the libcloog-ppl0 is not available; perhaps is should be?
I've been using the graphite optimizations for quite awhile, so I believe these are all problems recently introduced.
*** This bug has been marked as a duplicate of bug 317477 ***