Ya, 2.X zones were designed only with X/Y in mind. 3.0 zones, wide and open are designed with X/Y/Z in mind. Adding that extra dimension takes more work that just saying "Oh I'll just allow players to manipulate their Z positions".

Placing boundaries in the older zones isn't as easy as say putting Cheese on your sandwich because you decided you wanted to add it to your ham sandwich. It's more like Making a pizza and realizing you forgot to put the yeast in the dough. You can't really use that dough to make a pizza now, you have to start from scratch. While you might have the core ingredients on hand still, you still in a sense have to start back at square one in order to properly make flying zones.