I don't think that Beat Up pre-Gen IV was coded as a Dark-type physical move. However, I believe that the reason why Bulbapedia says that it uses physical Atk and Def is because the damage was typeless, which probably was probably physical.
This part is more speculation than concrete fact, but Beat-Up during that time likely was designed to make it seem like you're calling upon the other party members to attack. So rather than the Move being an Attack Move, it's more like a Status move that generates an Attack move for every party member. Rather than just being a multi-hit move, it's a multi-hit Metronome that chooses only one move. While it's categorized as a Dark-type offensive move, the specific coding must've made it disable the regular attack and skip to the weird typeless one.