The intension for this tool was fine tuning at the end of a process.
I can understand the whish but I am also more happy to have no "general" assumptions on folder structures. Well, in the end it is "only" a click to get everything in line (I still remember the time we didn't had the tool)
Take a look on Sigil if this is a show stopper for your work. Both applications have pros and cons depending on what is important for you and I knew not less people like myself who use both apps depending on what is need to do.