The wikis folder is just a shortcut to listing wikis. The Wikis section of the manual settings shows the wikis that are listed and you can manually add to that with wikis from anywhere that is accessible.
And at the top of the available wikis tab there is an interface for adding wikis using a variety of methods, you can make a new one, add an existing node/Bob wiki, create a new Bob wiki from a single file wiki or create a new Bob wiki from a collection of tiddlers in existing Bob wikis.
The wikis folder part came after that because adding all of the wikis manually got annoying.
I guess the part that is missing right now is when you make/add a new wiki it is placed in the wikis folder by default.
There is no reason you have to have multiple wikis, or to just use the index wiki for administration tasks. There are a lot of simplifications used by default with the single file executable version of Bob that makes some of this less clear.
I can make some things to do the copy move and delete parts. At the moment you can copy a wiki by creating a new wiki with all of the same tiddlers, or by using it as an edition to make a new wiki, but having a 'duplicate this wiki' button would probably be useful. The big reason that I haven't made the move and delete parts, aside from time, is that they would make it easy to accidentally lose data and I want to come up with some way that would help protect against that.