I'm attempting to do the same thing as the OP for my entire party that I registered in Pokemon Stadium back in the day. When I open the FLA save file dumped from the physical N64 cartridge in PKHeX, I see pokemon in the boxes, but it looks nothing like the pokemon that are in the registered sets in Pokemon Stadium. I can verify the FLA file is valid by opening the save file in Project64 and I can see the pokemon as they are meant to be.
Is there something I'm missing to get PkHeX to read the file correctly?
POKEMON STADIUM.fla