As far as I know, there are three sizes of holes. One is a very tiny hole, that holds flower stalk or a reed/water lily type plant. The second is a bigger hole that holds ferns, bushes, rocks, and small trees. There is a third size, the biggest one, you don't see as often. It holds the large cacti from the old western sets, and also the acacia trees that come with the new safari sets, as well as the old style acacia trees.
Can anyone else confirm this? I can't actually get to any of my plants and baseplates at the moment to double check, but I am about 95% sure of this.