It's applied in PACKAGECONFIG_CONFARGS variable and various bbclasses (and also various recipes) use this variable where needed, see git grep:
meta/classes/base.bbclass: appendVar('PACKAGECONFIG_CONFARGS', extraconf)
meta/classes/autotools.bbclass:EXTRA_OECONF_append = " ${PACKAGECONFIG_CONFARGS}"
meta/classes/cmake.bbclass:EXTRA_OECMAKE_append = " ${PACKAGECONFIG_CONFARGS}"
meta/classes/meson.bbclass:EXTRA_OEMESON += "${PACKAGECONFIG_CONFARGS}"
meta/classes/waf.bbclass:EXTRA_OECONF_append = " ${PACKAGECONFIG_CONFARGS}"
meta/recipes-graphics/glew/glew_2.1.0.bb:EXTRA_OEMAKE = "${PACKAGECONFIG_CONFARGS} \
It used to be included in EXTRA_OECONF by default, before: