A Pack'n Deploy tool is available from the vendor's website for customising the install but it's less than obvious to find, you have to pretend you want to evaluate & download the software and when you reach the download page the Pack'n Deploy tool is available in the same location.

Unfortunately configuration settings are stored in .ndb files rather than the registry (under ProgramData) - nhstconf.ndb was the only one that changed for the settings I used. Settings only appear to get saved once you exit from the program.

If you want to use stealth mode, after you have enabled it you will need to use Showhost.exe in the installation folder to access the UI. Remember this when you want to test that your package installed correctly.
 
I's not obvious how you disable the setup wizard that appears at first launch but I was advised by support that if you do it interactively the settings get saved into nhstconf.ndb and this seemed to work for me (the tool allows you to select the file for inclusion rather than providing an interface to apply all the settings you want). A few settings such as the license key are stored as properties.

Output is an .MSI and a .mst - your choice you can use the new .msi or the original with the .mst Support told me I needed both but the evidence indicates otherwise.