I could enable WebExtensions in Epiphany 43 by using dconf-editor, going to the following scheme:
/gnome/org/epiphany/web
and
enable the key:
enable-webextensions
BUT, none of the few extensions that did seem to be enabled and added to the browser seem to be properly loaded. None of them worked 
You might want to give this a try and if you get it to work, I would appreciate if you shared how.