In https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f53b263fb37b6029ac05878c70a11eca8513a60b Xinput was enabled by default. Xinput makes it impossible to disable smooth scrolling - the checkbox still there but it has no effect in firefox. This should be better indicated, maybe as a ebuild flag or at least in the buid message.
XINPUT has nothing to do with smooth scrolling checkbox. The latter is getting enabled via https://gitweb.gentoo.org/repo/gentoo.git/tree/www-client/firefox/files/gentoo-default-prefs.js by default but can be still disabled by user via UI.