The comments_open() boolean function return is filtered by ‘comments_open’. Untested, pseudo code as a guide:
add_filter( 'comments_open', function( $open ) {
$user = wp_get_current_user();
$open = $open && $user && time() - mysql2date( 'U', $user->user_registered ) > 3 * DAY_IN_SECONDS;
return $open;
} );
No guest users will be able to comment either, and I guess that is also what you want.