How to perform FileVault authenticated restart when updating OSX from AppStore? I am aware of the authenticated restart when using FileVault 2 on OS X. Running the fdesetup authrestart command does however restart the system immediately.

Now, when running the OS X Update from the App Store (which often requires restarting the system) the update process reboots the system automatically at "its own convenience". It prompts about the restart requirement before starting the whole update process and there is no "you should reboot now"-point in time.

Is there any way to "combine" OS X Update from the App Store with authenticated restart so that a remote system with system drive would not require manual drive unlocking from the console?
It sounds like you want the next restart, whenever it might occur, to skip FileVault authorization. You can use the -delayminutes option with a value of -1 for this.
From the fdesetup man page:

authrestart [-inputplist] [-delayminutes number_of_minutes_to_delay] [-verbose]

If FileVault is enabled on the current volume, it restarts the system, bypassing the initial unlock.   The optional -delayminutes option can be used to delay the restart command for a set number of minutes.  A value of 0 represents 'immediately', and a value of -1 represents 'never'.  The command may not work on all systems.

Try running the following command before the system update:
sudo fdesetup authrestart -delayminutes -1