OK, I just realized the correct xkb solution. I was trying out to map into different codes and FK1..12, but those are not F-row keys.
The solution with xkb is to map like so:
key <AE01> { [ 1, exclam, F1, F1 ] };
key <AE02> { [ 2, at, F2, F2 ] };
key <AE03> { [ 3, numbersign, F3, F3] };
key <AE04> { [ 4, dollar, F4, F4] };
key <AE05> { [ 5, percent, F5, F5] };
key <AE06> { [ 6, asciicircum, F6, F6] };
key <AE07> { [ 7, ampersand, F7, F7] };
key <AE08> { [ 8, asterisk, F8, F8] };
key <AE09> { [ 9, parenleft, F9, F9] };
key <AE10> { [ 0, parenright, KP_Home, KP_Home]};
And to add ISO_Level3_Shift code. In my case I use CAPS_LOCK for that and set it up in xmodmap:
nikola@work-x1c-mx19 ~ (master) » cat ~/.Xmodmap
! remove Caps Lock
clear lock
! add ISO_Level3_Shift
keycode 66 = ISO_Level3_Shift
! change PrtSc
keycode 107 = Menu NoSymbol Menu
Hope someone finds that helpful!