There are quite a few differences !
The first is that it can be run on a web server that is not the PC running Calibre (which applies to me)
More important is that that the Calibre server simply gives a flat structure consisting of a list of books. This program gives you a structure with a top level choice of Titles, Authors, Series. When you drill down a level it allows you to select between "All" or starting with a specific letter. You can now drill down another level. If going down the Authors path you can see which book belong to Series and which do not.
Basically it is more like the online catalog provided with Stanza. It makes handling large book collections much easier.