I doubt prototype board itself at 2006 because SEGA has been announced we have "remade" FZII based on System 16 in Fantazy Zone Complete Collection (FZCC), not "found (and ported/converted)" any prototype. SEGA made special PCB (and I heard these will be only 3 boards in the world) for the launch event for FZCC but it is at 2008, not 2006. FZCC project may even have not started at 2006.
And I have found the strings of "2008-07-15VER" in shinfz when select FZ2006II. The same strings is confirmed in ripped image from FZCC. So I'm convinced the ROM image in shinfz is based on 2008 version and doubt real release is 2006 printed on the screen.
[ATTACHED IMAGE - CLICK FOR FULL SIZE]
"Any company has no power to stop people emulating"
MAME is the emulator of no giving in the pressure from any company even if they don't allow