Isn't the .nv file interchangeable between cores? Or maybe, you could set the dip settings in the PC version and then move it to the Wii retroarch folder.
CPS-1/CPS-2 dip settings have not being available for me in those cores, at least on the Wii, only on main FBA core (i only tried once), as far as i can remember.
I tried to use the files generated by MAME on Windows in the NV folder and put them in RetroArch as xxxxx.nv files together with the roms but it didn't work. I must be missing something.