ISPConfig 3 will allow single and multiserver setups. This means all services may be on the same server like in ISPConfig 2 or the services may be spread to several servers and also there may be several servers of every type, e.g. 5 webservers, 2 mailservers, 1 database server that are controlled from within one controlpanel.
There where no commands send from one server to the others and there is no security problem with this. ISPConfig 3 uses either one central database server or replicated databases on the child servers. MySQL is able to encrypt the connections and if thats not secure enough for you, you may even setup mysql trogh a ssh tunnel or vpn.