Well, looking in the registry and comparing the registry before and after making those settings in Nero, there doesn't appear to be anything in the registry for those settings. Those settings don't even get saved.
The registry key that stores the "CD-ROM (Boot)" settings is HKEY_CURRENT_USER\Software\Ahead\Nero - Burning Rom\IsoBootDoc
What you could do is use CDRWIN (which saves the settings you need) or use CDIMAGE.EXE (command-line)
I prefer to use CDIMAGE.EXE because I just have a batch file:
BUILDISO.BAT
CODE
@PUSHD "%~dp0"
CDIMAGE.EXE -lW2PFPP_EN -h -n -d -bBOOTSECT.BIN -yt07C0 -m <PATH_TO_YOUR_FILES> "%SYSTEMDRIVE%\W2PFPP_EN.ISO"