The new <use> and <flag> options that were created by bug #199788 updating metadata.dtd need to be added as valid syntax for metadata.xml editing.
Err, are you sure that app-emacs/gentoo-syntax has anything to do with metadata.xml? The emacs aid for metadata.xml is nxml-mode together with nxml-gentoo-schemas.. and I did update the latter :)
No, this has nothing to do with app-{,x}emacs/gentoo-syntax, reassigning to vim team.
make.conf's syntax should also be updated to contain the current options in /usr/portage/profiles/desc This includes: ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CAMERAS CROSSCOMPILE_OPTS DVB_CARDS FOO2ZJS_DEVICES INPUT_DEVICES LCD_DEVICES LINGUAS LIRC_DEVICES MISDN_CARDS VIDEO_CARDS Stuff for the "bad" list: ELIBC KERNEL USERLAND
gentoo-syntax-20080717 has support for GLEP56 and includes the variables mentioned.