BuddyPress.org

Solution:

There is an action to hook to inside bp_core_activate_signup() that fires right after activating the account ( user clicked the link in the email ), so when the user hits /activate this will fire and reset the user_status to 3 ( 1 is spammer I guess ). Now to figure out the rest…

Here is the code ( the second function disallows the user from logging in with custom message ):

add_action( 'bp_core_activated_user', 'custom_bp_core_activated_user' );
function custom_bp_core_activated_user( $user ) {

	if ( empty( $user ) ) {
		
		return false;
	}

	if ( is_array($user) ) {
		
		$user_id = $user['user_id'];
	}
	else {
		
		$user_id = $user;
	}

	$member_type = bp_get_member_type($user_id);
	
	if ( $member_type == 'member_type_to_manually_activate' ) {
		
		global $wpdb;
		
		$wpdb->query( $wpdb->prepare( "UPDATE $wpdb->users SET user_status = 3 WHERE ID = %d", $user_id ) );
	}
}

add_filter( 'authenticate', 'custom_authenticate', 30 );
function custom_authenticate( $user ) {

	if ( is_wp_error( $user ) || empty( $user ) ) {

		return $user;
	}

	if ( 3 == $user->user_status ) {

		$member_type_name = bp_get_member_type($user->ID);
		$member_type = bp_get_member_type_object($member_type_name);
		
		return new WP_Error( 'invalid_username', __( '<strong>ERROR</strong>: All ' . $member_type->labels['name'] . ' accounts require manual confirmation from an admin. You might be contacted soon to verify your identity. You will recieve an email once your account is approved.', 'buddypress' ) );
	}

	return $user;
}