In the populate_network function, which is used by core multisite-convert, I observe the following code (line 1007 of wp-admin/includes/schema.php at v4.9.9):

if ( 1 == $network_id ) {
	$wpdb->insert( $wpdb->site, array( 'domain' => $domain, 'path' => $path ) );
	$network_id = $wpdb->insert_id;
} else {
	$wpdb->insert( $wpdb->site, array( 'domain' => $domain, 'path' => $path, 'id' => $network_id ) );
}

My understanding of the code in Core_Command.php is that multisite-convert is invoking populate_network(), and passing 1 as the site id ($network_id). As you can see, the WP core code then sets the network_id equal to the result of the INSERT query against wp_site. In most cases, this would be 1; however, if one has configured auto_increment_increment -- as is standard practice for database clusters -- then the wp_site table will store the site as id 4, and the code will generate the rest of the data using that same id.

From the perspective of core-command, this is mostly not a concern. However, it does appear that the constant SITE_ID_CURRENT_SITE is hardcoded with value 1. This produces an inconsistency between the config file and the database which is less than ideal. The solution is simple -- store the actual site_id/network_id and use that instead of a hardcoded 1. The only downside is that it means one extra database query (functions like get_main_network_id() appear to be accessing some kind of cache, or perhaps are falling back to default, and only return 1).