Hello! I was curious to find out if the newer version that came out with SNK's 40th Anniversary Collection is allowed on the board?

Your question goes more for Arcade version, and the answer is yes, the 40th anniv collection is quite suitable to play (especially in the Arcade Archives), but obviously you will need to wait when Arcade category could be created here before you submit your future runs, since NES runs are already here in this leaderboard @ProtoPugs