libSDL will not compile wayland backend without enabled gles flag. It's a result of fixing this bug https://bugs.gentoo.org/show_bug.cgi?id=504136. Could be easily reproduced by emerging >=libsdl-2.0.2-r1 with USE="wayland -gles". In consiguration stage there will be a "checking for Wayland support... no".
https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a13d06b93673ed218f9ebf96ad77214aed9d800d added: + wayland ( gles ) It should be 'wayland?' instead of 'wayland'. (Currently specified variant causes that both wayland and gles are always required.)
ug. let down by repoman. good catch. fixed now.