there is a very powerfull structure to define USE and CFLAGS in various areas: make.global, make.defaults, make.conf, environment (not sure if I'm up to date) so there might be +gnome -gnome +gnome -gnome during install you also have the chance to define make.conf in the /etc BEFORE chroot (by mistake) It would be very helpfull to allow an option emerge --displaysettings which would print out what the effective settings in the next emerge <package> run will be.
root@vapier root # grep USE_ORDER /etc/make.globals USE_ORDER="env:conf:auto:defaults"
root@vapier root # emerge info Portage 2.0.46-r5 (default-x86-1.4, gcc-2.95.3, glibc-2.3.1-r3) ================================================================= System uname: 2.4.20-lolo-r1_pre8 i686 Intel(R) Pentium(R) 4 CPU 1.80GHz GENTOO_MIRRORS="http://www.ibiblio.org/pub/Linux/distributions/gentoo" CONFIG_PROTECT="/etc /var/qmail/control /usr/kde/2/share/config /usr/kde/3/share/config /usr/kde/3.1/share/config /usr/share/config" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" PORTDIR="/usr/portage" DISTDIR="/usr/portage/distfiles" PKGDIR="/root/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR_OVERLAY="/usr/local/portage" USE="x86 cdr scanner -3dfx -3dnow aalib -acl -afs -alsa apm -arts -atlas avi -berkdb -bonobo -canna -cjk crypt cups dga directfb -doc dvd encode esd -evo fbcon flash -freewnn -gb gd gdbm ggi -ggz gif -gnome -gnome-libs gphoto2 gpm gtk gtk2 -gtkhtml -guile -icc -icc-pgo imap imlib -innodb ipv6 java jpeg kde kerberos -lcms -ldap -libg++ -libgda libwww -matrox -maildir -mbox -mikmod mmx -motif mozilla mpeg -mule mysql nas ncurses -nls nocardbus -oci8 -odbc oggvorbis opengl -oss pam -pcmcia pda pdflib perl pic plotutils png pnp -postgres python qt qtmt quicktime readline -ruby samba sasl sdl -slang slp snmp socks5 spell sse ssl static svga tcltk tcpd -tetex tiff truetype -trusted -voodoo3 wavelan X -xface xml xml2 xmms xv -zeo zlib" COMPILER="gcc3" CHOST="i686-pc-linux-gnu" CFLAGS="-march=pentium4 -O9 -pipe" CXXFLAGS="-march=pentium4 -O9 -pipe" ACCEPT_KEYWORDS="x86 ~x86" MAKEOPTS="-j2" AUTOCLEAN="yes" SYNC="rsync://rux0r/gentoo-portage" FEATURES="sandbox ccache noauto"