All those extra tiles

They are the new enemy tiles, as well as an updated tile set. Delete them if you don't want to use them.
(Enemy tiles are for the New Enemy Tiles rule)

Whats that then, the new enemy tiles rule?

Yes. It makes it easier to do the enemy animations, as well as allowing long animations.
The new enemy tiles.pdf file has the tile #s for all the enemies, making it a snap to edit/make those tiles.

What I meant was, what does it do when you check the New Enemy Tiles rule.

How is it different from using the older way of doing enemies?

If you use the new enemy tiles, it uses different tiles for every direction an enemy moves. I'm pretty sure it also uses multiple tiles for animations that are otherwise made by flipping a single tiles, like that of a Stalfos.

It uses all those extra enemy tiles you were asking about. It ends up with like 25 or 30 pages of tiles just for enemy animations, so you have some room to animate them well.

24 to be exact. I had nothing to do but count them on the way down to getting some combos from Prince MSC's Mystic Land tileset. That is a good quality set, but missing a few nuts n' bolts.

And there is way more than enough room to animate things with the amazing 125 pages of tiles. Looking down there is like looking off of a skyscraper. (I wish I wouldn't puke so much around page 117. -kidding.)