@moonman In the User::register function they get set manually with the following comment:
// Set default-on options here, otherwise they'll be disabled
// initially for sites using caching, since the initial encache
// doesn't know about the defaults in the database.
Those values should probably actually be set from a site-wide configuration option instead. Feel free to make a merge request for it, otherwise I'll probably fix it sometime. Got a lot of work the coming days though.