The solution should be that required Domino updates are aligned with the server core setup. Regardless which server you have installed (Enterprise, Utility, Custom), the Feature Pack installer does not take this in account but installs everything.
An option could be to look-up " /domprg/.install.dat", where the components installed with the core server setup are logged.
+ custom setup does not seem to work on Linux silent install
+ only install what is really necessary (e.g Utility server is not licensed for messaging but the complete iNotes packages becomes installed.