MacBook Pro Function key + Command/Option hotkeys problem [duplicate]
Sharing a solution to this problem, although it's pretty uncommon case. Root cause of the problem was Karabiner elements setup. They have a ticket open corresponding to this case: https://github.com/tekezo/Karabiner-Elements/issues/1160
What you need to do to start registering this hotkeys is essentially enable unknown devices in Karabiner settings.