The opponents in the start of the waterfall cave are a lower level that the flying fortresses, so you will not get much experience from them if you leave it too long.
There is a cave near the source of the shorter waterfall across from the grand knight teleporter shrine, as well, though I don't know if the teleporter stone gets disabled / enabled for the boss fight there.
In Divine Divinity there were teleporter pads pretty much the same as the D2:ED teleporter shrines, and teleporter pyramids (similar to the dragon stone, but you could place one wherever you wanted, and keep the other on you to teleport back to base whenever you wished, except in certain regions or during cutscenes, etc). There were also pairs of teleporter stones which teleported you between specific locations; in a continuous region battle tower, something similar could be used to allow quick travel between different platforms. I assume in D2:ED it was easier to allow the platforms to be upgraded if each one was a separate area (or something).