If you are going to update existing installations, it all depends on what you select in the last step of the configuration process. Basically, you have three options - update everything, update everything except security settings (i.e. passwords and permissions), or skip updating settings (in which case only the program files themselves will be updated). There is a table on the page that lists all possible combinations, see the link above.
Here by "updating" I mean not only product version update, but also deploying a new package of the same version, which might be the case if you want to update Host settings on already deployed Hosts.
Let me clarify by previous post. I assume that you use the MSI Configurator to build/configure your custom Host installer before the deployment. If you don't, (i.e. if you deploy the vanilla Host) won't be able to have the Internet-ID code get generated automatically, since in the vanilla Host this option is turned off by default.
By default, none of the hosts acquire an Internet-ID from custom server automatically. I have to right-click host icon in taskbar, click on Internet-ID connection settings, enter configuration password and click a button to get a new ID. I want this to be done by default.