I tried to build emacs with USE="gtk3 -gtk", but it did not even enable gtk. I did not know, that gtk3 doesn't make sence without gtk flag, and it is not announced during emerge. They need to be in REQUIRED_USE: (gtk3? (gtk)). Or even make them mutually exclusive (?? (gtk3 gtk))... Some relatively rare software have options to build UI modules for both gtk3 and gtk2, so would be more consistent to have gtk & gtk3 use flags not requiring each other (don't remember, if emacs can build with both - may be make them mutually exclusive). By the way, i was told in one place, that they now prefer gtk flag to use current official version (3), while versioned (gtk2) is for older (alsa why they argued agains gtk3 use flag - can't remember where discussion was, for reference). So, it could be also (?? (gtk gtk2)).
Unfortunately, the precise meaning of the gtk/gtk2/gtk3 flags is still an open issue. There is a QA policy draft, but it is not yet in force: https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Policies#gtk.2Fgtk2.2Fgtk3_USE_flag_situation Unless that policy is settled, we won't touch the gtk and gtk3 flags in Emacs ebuilds, and their meaning will be as described: gtk - Add support for x11-libs/gtk+ (The GIMP Toolkit) gtk3 - Prefer version 3 of the GIMP Toolkit to version 2 (x11-libs/gtk+) That is, with USE="-gtk" you'll get no GTK support. The ebuild doesn't output a warning for the USE="-gtk gtk3" configuration, because +gtk3 is enabled by IUSE default (so users would get the warning even if they don't have gtk3 explicitly enabled, which would be confusing).