Because it was altered in development to the point where we consider it a different game. It isn't just a matter of inaccurate emulation, the actual programming of the game was changed to patch glitches and to alter physics, graphics, among other things. There is a separate leaderboard for the 3D classics version if you want to run it.

One example off the top of my head is how Kirby preserves momentum after taking damage off of spikes. This makes the normal strategy for the beginning of 5-4 not work.